Genome Assembly workshop

Software List

• Velvet 

Current version 1.2.10

Source code in C language

https://www.ebi.ac.uk/~zerbino/velvet/

• VelvetOptimiser 

Current version 2.2.5

Perl script

Requirements

•   Velvet >= 0.7.51 (including 1.x series)  : Velvet 1.2.10

•   Perl >= 5.8 

•   BioPerl >= 1.4 

http://www.vicbioinformatics.com/software.velvetoptimiser.shtml

• SPAdes 

Current version 3.12

Executable files (Linux 64 bits and MacOSx) and Source code

http://cab.spbu.ru/software/spades/

• MaSuRCA 

Current version 3.2.8

 Source code in C language

 https://github.com/alekseyzimin/masurca

Raw data

Use a part of Chr11 of Solanum lycopersicum (Tomato)
Chr11 ~53 Mbp -> ~ 4.8 Mbp
       Generate simulated illumina Paired-end FASTQ files
  • 151 bp paired-end reads
  • Insertion length 300 bp

Location : /home/chumpol/AssemblyWS

• FASTA -> Reference sequence in FASTA formatted (cabV2.fa)

• FASTQ -> illumina paired-end reads in FASTQ formatted (cabV2_read1.fq.gz, cabV2_read2.fq.gz)

Preparing storage for raw reads

  • Login to server (158.108.144.7)
In [ ]:
ssh annotest@158.108.144.7
  • Create the directory for workshop
    • In [ ]:
    mkdir AssemblyWS
    In [31]:
    dirWS = "/home/annotest/AssemblyWS"
    In [32]:
    cd {dirWS}

    /home/annotest/AssemblyWS
    In [34]:
    %%bash
ln -s /home/chumpol/AssemblyWS/FASTQ .
    In [ ]:
    %%bash
ln -s /home/chumpol/AssemblyWS/FASTA .
  • Check raw data directory
    • In [39]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 30 Aug  7 15:52 FASTA -> /home/chumpol/AssemblyWS/FASTA/
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 30 Aug  7 15:52 FASTQ -> /home/chumpol/AssemblyWS/FASTQ/

    Velvet Assembler

    • Check the velvet executable files (velveth and velvetg)
    In [14]:
    %%bash
velveth

    velveth - simple hashing program
Version 1.2.10

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Compilation settings:
CATEGORIES = 6
MAXKMERLENGTH = 250
OPENMP
LONGSEQUENCES
BIGASSEMBLY

Usage:
./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]

	directory	: directory name for output files
	hash_length	: EITHER an odd integer (if even, it will be decremented) <= 250 (if above, will be reduced)
			: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 250 (if above, will be reduced)
				and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
	filename	: path to sequence file or - for standard input

File format options:
	-fasta	-fastq	-raw	-fasta.gz	-fastq.gz	-raw.gz	-sam	-bam	-fmtAuto
	(Note: -fmtAuto will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2

File layout options for paired reads (only for fasta and fastq formats):
	-interleaved	: File contains paired reads interleaved in the one file (default)
	-separate	: Read 2 separate files for paired reads

Read type options:
	-short	-shortPaired
	...
	-short5	-shortPaired5
	-short6	-shortPaired6
	-long	-longPaired
	-reference

Options:
	-strand_specific	: for strand specific transcriptome sequencing data (default: off)
	-reuse_Sequences	: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-reuse_binary	: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
	-noHash			: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
	-create_binary  	: create binary CnyUnifiedSeq file (default: off)

Synopsis:

- Short single end reads:
	velveth Assem 29 -short -fastq s_1_sequence.txt

- Paired-end short reads (remember to interleave paired reads):
	velveth Assem 31 -shortPaired -fasta interleaved.fna

- Paired-end short reads (using separate files for the paired reads)
	velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

- Two channels and some long reads:
	velveth Assem 43 -short -fastq unmapped.fna -longPaired -fasta SangerReads.fasta

- Three channels:
	velveth Assem 35 -shortPaired -fasta pe_lib1.fasta -shortPaired2 pe_lib2.fasta -short3 se_lib1.fa

Output:
	directory/Roadmaps
	directory/Sequences
		[Both files are picked up by graph, so please leave them there]
  • Create directory for running Velvet
    • In [41]:
    mkdir Velvet
  • Change directory to Velvet directory, create symbolic links of FASTQ files
    • In [47]:
    dirVelvet = "/home/annotest/AssemblyWS/Velvet"
    In [48]:
    cd {dirVelvet}

    /home/annotest/AssemblyWS/Velvet
    In [52]:
    %%bash
ln -s ../FASTQ/* .
    In [53]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:00 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:00 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Create shell script to run velvet (Run_Velvet.sh) with Nano / copy Run_Velvet.sh from /home/chumpol/AssemblyWS/Velvet/Run_Velvet.sh
    • In [54]:
    %%bash
cp /home/chumpol/AssemblyWS/Velvet/Run_Velvet.sh .
    In [55]:
    %%bash
more Run_Velvet.sh

    ::::::::::::::
Run_Velvet.sh
::::::::::::::
#!/bin/bash

# $1 as k-mer
# $2 input read

velveth Test_${1} $1 -fastq.gz -shortPaired -separate ${2}_read1.fq.gz ${2}_read2.fq.gz
velvetg Test_${1} -ins_length 300 -exp_cov 10 -cov_cutoff auto -min_contig_lgth 1000

    Parameters

    k-mers           : k-mers as first parameter ($1) of the script
-fastq.gz        : format of read files
-shortPaired -separate :  read type (Paired-end)
       Filename       : ${2} as second parameter of the script
-ins_length     : expected distance between two paired-end reads (300) 
-exp_cov        : expected coverage to infer (10)
      -cov_cutoff      : removal of low coverage nodes (auto)
      -min_contig_lgth : minimum contig length exported to contigs.fa file.
      Output is saved in Test_${1}
  • Run scripts
    • In [58]:
    %%bash
./Run_Velvet.sh 75 cabV2

    [0.000000] Reading FastQ file cabV2_read1.fq.gz;
[0.000291] Reading FastQ file cabV2_read2.fq.gz;
[5.013386] 925060 sequences found in total in the paired sequence files
[5.013390] Done
[5.026487] Reading read set file Test_75/Sequences;
[5.203390] 925060 sequences found
[5.976033] Done
[5.976037] 925060 sequences in total.
[5.976143] Writing into roadmap file Test_75/Roadmaps...
[6.359098] Inputting sequences...
[6.365410] Inputting sequence 0 / 925060
[8.983243]  === Sequences loaded in 2.624489 s
[8.985614] Done inputting sequences
[8.985616] Destroying splay table
[9.372377] Splay table destroyed
[0.000000] Reading roadmap file Test_75/Roadmaps
[1.225080] 925060 roadmaps read
[1.237108] Creating insertion markers
[1.393650] Ordering insertion markers
[1.419950] Counting preNodes
[1.559739] 1677039 preNodes counted, creating them now
[6.524007] Adjusting marker info...
[6.661250] Connecting preNodes
[7.019085] Cleaning up memory
[7.020495] Done creating preGraph
[7.020504] Concatenation...
[7.563851] Renumbering preNodes
[7.563894] Initial preNode count 1677039
[7.622448] Destroyed 1260839 preNodes
[7.622453] Concatenation over!
[7.622455] Clipping short tips off preGraph
[7.739048] Concatenation...
[7.911339] Renumbering preNodes
[7.911342] Initial preNode count 416200
[7.916685] Destroyed 392546 preNodes
[7.916687] Concatenation over!
[7.916687] 199487 tips cut off
[7.916688] 23654 nodes left
[7.916800] Writing into pregraph file Test_75/PreGraph...
[8.257118] Reading read set file Test_75/Sequences;
[8.435761] 925060 sequences found
[9.232938] Done
[9.638351] Reading pre-graph file Test_75/PreGraph
[9.638415] Graph has 23654 nodes and 925060 sequences
[9.802831] Scanning pre-graph file Test_75/PreGraph for k-mers
[9.957928] 5166917 kmers found
[10.568908] Sorting kmer occurence table ... 
[15.315342] Sorting done.
[15.315346] Computing acceleration table... 
[15.466536] Computing offsets... 
[15.604930] Ghost Threading through reads 0 / 925060
[16.031517]  === Ghost-Threaded in 0.441526 s
[16.031861] Threading through reads 0 / 925060
[17.042687]  === Threaded in 1.011161 s
[17.113997] Correcting graph with cutoff 0.200000
[17.117678] Determining eligible starting points
[17.146119] Done listing starting nodes
[17.146121] Initializing todo lists
[17.149003] Done with initilization
[17.149005] Activating arc lookup table
[17.152900] Done activating arc lookup table
[17.553726] 10000 / 23654 nodes visited
[17.930653] 20000 / 23654 nodes visited
[18.017725] Concatenation...
[18.018440] Renumbering nodes
[18.018441] Initial node count 23654
[18.018827] Removed 19478 null nodes
[18.018832] Concatenation over!
[18.018833] Clipping short tips off graph, drastic
[18.019700] Concatenation...
[18.043709] Renumbering nodes
[18.043710] Initial node count 4176
[18.043861] Removed 1023 null nodes
[18.043862] Concatenation over!
[18.043862] 3153 nodes left
[18.043953] Writing into graph file Test_75/Graph2...
[18.666390] Measuring median coverage depth...
[18.667539] Median coverage depth = 10.295438
[18.667582] Removing contigs with coverage < 5.147719...
[18.669440] Concatenation...
[18.714441] Renumbering nodes
[18.714442] Initial node count 3153
[18.714514] Removed 2090 null nodes
[18.714515] Concatenation over!
[18.714555] Concatenation...
[18.714631] Renumbering nodes
[18.714631] Initial node count 1063
[18.714633] Removed 0 null nodes
[18.714633] Concatenation over!
[18.714640] Clipping short tips off graph, drastic
[18.714741] Concatenation...
[18.715255] Renumbering nodes
[18.715256] Initial node count 1063
[18.715295] Removed 37 null nodes
[18.715296] Concatenation over!
[18.715296] 1026 nodes left
[18.715297] Read coherency...
[18.715305] Identifying unique nodes
[18.715334] Done, 791 unique nodes counted
[18.715335] Trimming read tips
[18.715424] Renumbering nodes
[18.715424] Initial node count 1026
[18.715426] Removed 0 null nodes
[18.715426] Confronted to 0 multiple hits and 0 null over 0
[18.715427] Read coherency over!
[18.722075] Starting pebble resolution...
[18.732289] Computing read to node mapping array sizes
[18.757604] Computing read to node mappings
[18.768573] Estimating library insert lengths...
[18.774250] Done
[18.774260] Computing direct node to node mappings
[18.788234] Scaffolding node 0
[18.798856]  === Nodes Scaffolded in 0.024595 s
[18.809034] Preparing to correct graph with cutoff 0.200000
[18.920196] Cleaning memory
[18.920267] Deactivating local correction settings
[18.920313] Pebble done.
[18.920314] Starting pebble resolution...
[18.929721] Computing read to node mapping array sizes
[18.949847] Computing read to node mappings
[18.962627] Estimating library insert lengths...
[18.972112] Done
[18.972119] Computing direct node to node mappings
[18.993819] Scaffolding node 0
[19.005947]  === Nodes Scaffolded in 0.033822 s
[19.014262] Preparing to correct graph with cutoff 0.200000
[19.020280] Cleaning memory
[19.020284] Deactivating local correction settings
[19.020312] Pebble done.
[19.020313] Concatenation...
[19.029035] Renumbering nodes
[19.029037] Initial node count 1026
[19.029114] Removed 631 null nodes
[19.029123] Concatenation over!
[19.029124] Removing reference contigs with coverage < 5.147719...
[19.029158] Concatenation...
[19.029170] Renumbering nodes
[19.029171] Initial node count 395
[19.029172] Removed 0 null nodes
[19.029178] Concatenation over!
[19.034808] Writing contigs into Test_75/contigs.fa...
[19.691495] Writing into stats file Test_75/stats.txt...
[19.696405] Writing into graph file Test_75/LastGraph...
[20.341936] Estimated Coverage cutoff = 5.147719
Final graph has 395 nodes and n50 of 55255, max 171853, total 4594714, using 860030/925060 reads

    The final contigs.fa is saved in Test_75 directory.

  • Try with another k-mers, such as 71, 81.

    • VelvetOptimiser

    Multi-threaded Perl script for automatically optimizing the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet assembler.

    • Create directory for running VelvetOptimiser
    In [59]:
    cd ..

    /home/annotest/AssemblyWS
    In [60]:
    pwd
    Out[60]:
    '/home/annotest/AssemblyWS'
    In [61]:
    mkdir VelvetOptimiser
  • Change directory to working directory, create symbolic links of FASTQ files.
    • In [62]:
    cd VelvetOptimiser

    /home/annotest/AssemblyWS/VelvetOptimiser
    In [63]:
    %%bash
ln -s ../FASTQ/* .
    In [64]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:06 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:06 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Create shell script to run VelvetOptimiser (Run_VelvetOptimiser.sh) with Nano / copy Run_VelvetOptimiser.sh from

    • /home/chumpol/AssemblyWS/VelvetOptimiser/Run_VelvetOptimiser.sh

    In [65]:
    cp /home/chumpol/AssemblyWS/VelvetOptimiser/Run_VelvetOptimiser.sh .
    In [66]:
    cat Run_VelvetOptimiser.sh

    #!/bin/env bash


# $1 is number of threads
# $2 is start k-mers
# $3 is stop k-mers
# $4 is read name

# Start from $1 to $2, step 5
/share/apps/VelvetOptimiser/VelvetOptimiser.pl -t $1 -s $2 -e $3 -x 5 -f "-shortPaired -separate -fastq.gz ${4}_read1.fq.gz ${4}_read2.fq.gz" -o "-ins_length 300 -exp_cov 10 -cov_cutoff auto -min_contig_lgth 1000"

    Parameters

     -t #        : number of CPU threads to use
 -s #        : start k-mers
 -e #        : stop k-mers
 -x #        : incremental steps of k-mers
 -f “string” : velveth parameters
 -o “string” : velvetg parameters
  • Run the scripts
    • In [67]:
    %%bash
./Run_VelvetOptimiser.sh 16 85 91 cabV2

    Logfile name: 07-08-2018-16-09-58_Logfile.txt

    ****************************************************
           VelvetOptimiser.pl Version 2.3.0-alpha
****************************************************
Number of CPUs available: 144
Current free RAM: 996.047GB
Velvet OMP compiler setting: 1
Aug  7 16:09:58 Starting to check input parameters.
	Old hash step value 5
	Hash search step value was odd, substracting one.  New hash step value = 4
	Velveth parameter string OK.
Aug  7 16:09:58 Finished checking input parameters.
Velvet details:
	Velvet version: 1.2.10
	Compiled categories: 6
	Compiled max kmer length: 250
	Maximum number of Velvet instances to run: 16
Will run velvet optimiser with the following paramters:
	Velveth parameter string:
		-shortPaired -separate -fastq.gz cabV2_read1.fq.gz cabV2_read2.fq.gz
	Velveth start hash values:	85
	Velveth end hash value:		91
	Velveth hash step value:	4
	Velvetg minimum coverage cutoff to use:	0

	Read tracking for final assembly off.
Aug  7 16:09:58 Beginning velveth runs.
Aug  7 16:09:58		Running velveth with hash value: 85.
Aug  7 16:10:00		Running velveth with hash value: 89.
Aug  7 16:10:03		Running velveth with hash value: 91.
Aug  7 16:10:09		Velveth with hash value 85 finished.
Aug  7 16:10:10		Velveth with hash value 89 finished.
Aug  7 16:10:13		Velveth with hash value 91 finished.
Aug  7 16:10:13 Finished velveth runs.
Aug  7 16:10:13 Beginning vanilla velvetg runs.
Aug  7 16:10:13		Running vanilla velvetg on hash value: 85
Aug  7 16:10:15		Running vanilla velvetg on hash value: 89
Aug  7 16:10:18		Running vanilla velvetg on hash value: 91
Aug  7 16:10:35		Velvetg on hash value: 85 finished.
Aug  7 16:10:36		Velvetg on hash value: 89 finished.
Aug  7 16:10:37		Velvetg on hash value: 91 finished.
Aug  7 16:10:37 Hash value of best assembly by assembly score: 91
Aug  7 16:10:37 Optimisation routine chosen for best assembly: shortPaired
Aug  7 16:10:37 Looking for the expected coverage
Aug  7 16:10:39		Expected coverage set to 7
Aug  7 16:10:39 Setting assembly short insert length(s) to auto
Aug  7 16:10:39 Beginning coverage cutoff optimisation
Aug  7 16:10:40		Setting cov_cutoff to 3.461.
Aug  7 16:10:44		Setting cov_cutoff to 2.139.
		Looking for best cutoff score between 0.000 and 5.600
		Max cutoff lies between 0.000 & 3.461
		fc = 4615188	fd = 4615398	abs diff = 210
Aug  7 16:10:47		Setting cov_cutoff to 1.322.
		Max cutoff lies between 0.000 & 2.139
		fc = 4615398	fd = 4615500	abs diff = 102
Aug  7 16:10:51		Setting cov_cutoff to 0.817.
		Max cutoff lies between 0.000 & 1.322
		fc = 4615500	fd = 4615500	abs diff = 0
Aug  7 16:10:54		Setting cov_cutoff to 0.505.
		Max cutoff lies between 0.505 & 1.322
		fc = 4615500	fd = 4615399	abs diff = 101
Aug  7 16:10:58		Setting cov_cutoff to 1.010.
		Optimum value of cutoff is 1.32
		Took 5 iterations
Aug  7 16:11:02


Final optimised assembly details:
********************************************************
Assembly id: 3
Assembly score: 4615405
Velveth timestamp: Aug  7 2018 16:10:13
Velvetg timestamp: Aug  7 2018 16:11:02
Velveth version: 1.2.10
Velvetg version: 1.2.10
Readfile(s): -shortPaired -separate -fastq.gz cabV2_read1.fq.gz cabV2_read2.fq.gz
Velveth parameter string: auto_data_91 91 -shortPaired -separate -fastq.gz cabV2_read1.fq.gz cabV2_read2.fq.gz
Velvetg parameter string: auto_data_91 -ins_length 300 -exp_cov 7 -cov_cutoff auto -min_contig_lgth 1000 -clean yes
Assembly directory: /home/annotest/AssemblyWS/VelvetOptimiser/auto_data_91
Velvet hash value: 91
Roadmap file size: 40716059
Total number of contigs: 345
n50: 22892
length of longest contig: 112538
Total bases in contigs: 4615405
Number of contigs > 1k: 345
Total bases in contigs > 1k: 4615405
Paired Library insert stats:
**********************************************************


Assembly output files are in the following directory:
/home/annotest/AssemblyWS/VelvetOptimiser/auto_data_91
    • Use 16 CPU cores
    • Vary k-mers from 75 - 91

    SPAdes assembler

    • Create directory for running SPAdes
    In [91]:
    cd ..

    /home/annotest/AssemblyWS
    In [71]:
    mkdir SPAdes
  • Change directory to working directory, create symbolic links of FASTQ files.
    • In [72]:
    cd SPAdes

    /home/annotest/AssemblyWS/SPAdes
    In [73]:
    %%bash
ln -s ../FASTQ/* .
    In [74]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:14 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:14 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Create shell script to run SPAdes (Run_SPAdes.sh) with Nano / copy Run_SPAdes.sh from

    • /home/chumpol/AssemblyWS/SPAdes/Run_SPAdes.sh

    In [75]:
    cp /home/chumpol/AssemblyWS/SPAdes/Run_SPAdes.sh .
    In [76]:
    cat Run_SPAdes.sh

    #!/bin/bash

# $1 as number of threads
# $2 as input file
# $3 as output directory

/share/apps/SPAdes-3.12.0-Linux/bin/spades.py -t $1 -1 ${2}_read1.fq.gz -2 ${2}_read2.fq.gz --only-assembler --cov-cutoff auto --careful -o $3

    Parameters

    -t #             : number of CPU threads to use
-1 file1         : paired read1 file
-2 file2         : paired read2 file
--only-assembler : runs only assembling (without read error correction)
--careful        : tries to reduce number of mismatches and short indels
-o output        : output directory
  • Run the script
    • In [77]:
    %%bash
./Run_SPAdes.sh 16 cabV2 SPAdes_Out

    Command line: /share/apps/SPAdes-3.12.0-Linux/bin/spades.py	-t	16	-1	/home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz	-2	/home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz	--only-assembler	--cov-cutoff	auto	--careful	-o	/home/annotest/AssemblyWS/SPAdes/SPAdes_Out	

System information:
  SPAdes version: 3.12.0
  Python version: 3.5.5
  OS: Linux-3.10.0-514.26.2.el7.x86_64-x86_64-with-centos-7.4.1708-Core

Output dir: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz']
      right reads: ['/home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned ON
  MismatchCorrector will be used
  Coverage cutoff is turned ON and threshold will be auto-detected
Other parameters:
  Dir for temp files: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp
  Threads: 16
  Memory limit (in Gb): 250


======= SPAdes pipeline started. Log can be found here: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/spades.log


===== Assembling started.


== Running assembler: K21

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K21/configs/config.info
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K21/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=21
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  77)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  78)   Converting paired reads
  0:00:00.311    80M / 80M   INFO    General                 (binary_converter.hpp      :  93)   16384 reads processed
  0:00:00.557    96M / 96M   INFO    General                 (binary_converter.hpp      :  93)   32768 reads processed
  0:00:01.046   124M / 124M  INFO    General                 (binary_converter.hpp      :  93)   65536 reads processed
  0:00:02.009   180M / 180M  INFO    General                 (binary_converter.hpp      :  93)   131072 reads processed
  0:00:03.491   296M / 296M  INFO    General                 (binary_converter.hpp      :  93)   262144 reads processed
  0:00:07.294   468M / 468M  INFO    General                 (binary_converter.hpp      : 117)   462530 reads written
  0:00:07.844     4M / 468M  INFO    General                 (read_converter.hpp        :  87)   Converting single reads
  0:00:07.937   132M / 468M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:07.937     4M / 468M  INFO    General                 (read_converter.hpp        :  95)   Converting merged reads
  0:00:08.025   132M / 468M  INFO    General                 (binary_converter.hpp      : 117)   0 reads written
  0:00:08.027     4M / 468M  INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:08.027     4M / 468M  INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:08.027     4M / 468M  INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:08.027     4M / 468M  INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:08.027     4M / 468M  INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:08.027     4M / 468M  INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:08.027     4M / 468M  INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 262144
  0:00:12.163     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:12.163     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:12.853    64M / 8G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:12.853    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:13.006    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 18798949 kmers in total.
  0:00:13.007    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:13.225    64M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:13.225    64M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:13.225    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:13.225    64M / 8G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:13.225    64M / 8G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:13.225    64M / 8G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 262144
  0:00:16.612     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 18798949 kmers
  0:00:16.612     8G / 8G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 18798949 kmers.
  0:00:17.289    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:17.435    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 18304331 kmers in total.
  0:00:17.435    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:17.613    64M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:18.206    64M / 8G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:18.388    64M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 8496152 bytes occupied (3.71329 bits per kmer).
  0:00:18.402    84M / 8G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:19.421    84M / 8G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:19.421    84M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Early tip clipping
  0:00:19.421    84M / 8G    INFO    General                 (construction.cpp          : 253)   Early tip clipper length bound set as (RL - K)
  0:00:19.421    84M / 8G    INFO   Early tip clipping       (early_simplification.hpp  : 181)   Early tip clipping
  0:00:21.321    84M / 8G    INFO   Early tip clipping       (early_simplification.hpp  : 184)   3269566 22-mers were removed by early tip clipper
  0:00:21.321    84M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:21.322    84M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:22.161   128M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 1390562 sequences extracted
  0:00:22.689   128M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:22.898   132M / 8G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:23.321   448M / 8G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:23.321   448M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:23.321   448M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:23.720   456M / 8G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 8725488 bytes occupied (3.71318 bits per kmer).
  0:00:23.747   528M / 8G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:25.616   528M / 8G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:26.337   528M / 8G    INFO    General                 (construction.cpp          : 464)   Processed 2781021 edges
  0:00:26.423   420M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 2
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 21
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 23. Coverage mad: 7.413
  0:00:26.424   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:26.467   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:26.589   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:27.025   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:27.959   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 22.4523. Fitted coverage std. dev: 5.4301
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.872896
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 5
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 5
  0:00:28.568   420M / 8G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4603800
  0:00:28.568   420M / 8G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 22.4523
  0:00:28.568   420M / 8G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 5
  0:00:28.569   420M / 8G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 1
  0:00:28.569   420M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:28.569   420M / 8G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:28.569   420M / 8G    INFO    General                 (graph_simplification.hpp  : 662)   Flanking coverage based disconnection disabled
  0:00:28.569   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:28.666   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 0 times
  0:00:28.666   420M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:28.666   420M / 8G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:28.666   420M / 8G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:28.667   420M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:28.667   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:28.831   404M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 466 times
  0:00:28.831   404M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:58.961   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 460110 times
  0:00:58.961   420M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:58.987   428M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:58.987   428M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:00:58.987   428M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 175 times
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:59.041   392M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:59.529   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 16646 times
  0:00:59.529   340M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:00:59.529   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.542   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 143 times
  0:00:59.542   340M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.172   316M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 3842 times
  0:01:00.172   316M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.208   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 1014 times
  0:01:00.208   308M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:01:00.208   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.212   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.212   308M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.288   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 129 times
  0:01:00.288   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.303   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 516 times
  0:01:00.303   304M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:01:00.303   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.304   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 1 times
  0:01:00.304   304M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.335   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 80 times
  0:01:00.335   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 62 times
  0:01:00.338   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.338   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.345   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 15 times
  0:01:00.345   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 54 times
  0:01:00.346   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.346   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.350   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 8 times
  0:01:00.350   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 18 times
  0:01:00.352   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 3 times
  0:01:00.352   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 26 times
  0:01:00.353   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.353   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 2 times
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 11 times
  0:01:00.354   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:00.354   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.355   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 19 times
  0:01:00.355   300M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:01:00.355   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.359   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.359   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.459   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 110 times
  0:01:00.459   300M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:00.464   296M / 8G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:00.464   296M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:01:00.464   296M / 8G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:01:00.464   296M / 8G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:01:00.464   296M / 8G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:01:00.464   296M / 8G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:01:00.464   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.468   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.468   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.547   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 9 times
  0:01:00.547   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.550   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.550   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:00.624   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:00.624   296M / 8G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:01:00.646   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:01:00.648   296M / 8G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 0 times
  0:01:00.648   296M / 8G    INFO    General                 (simplification.cpp        : 340)   Removing all the edges having coverage 1 and less
  0:01:00.651   296M / 8G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:00.659   296M / 8G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 25.6143
  0:01:00.659   296M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:00.659   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph_with_scaffolds.gfa
  0:01:00.772   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/before_rr.fasta
  0:01:00.902   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph.fastg
  0:01:01.376   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/simplified_contigs.fasta
  0:01:01.511   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/final_contigs.fasta
  0:01:01.645   296M / 8G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:01.645   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph_with_scaffolds.gfa
  0:01:01.762   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/before_rr.fasta
  0:01:01.893   296M / 8G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/assembly_graph.fastg
  0:01:02.369   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/simplified_contigs.fasta
  0:01:02.508   296M / 8G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K21/final_contigs.fasta
  0:01:02.655   296M / 8G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:01:02.951    64M / 8G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 1 minutes 2 seconds
Max read length detected as 151
Default k-mer sizes were set to [21, 33, 55, 77] because estimated read length (151) is equal to or greater than 150

== Running assembler: K33

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K33/configs/config.info
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K33/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=33
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  59)   Binary reads detected
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:00.002     4M / 4M    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.002     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:00.002     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:04.181     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:04.181     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:06.101    64M / 9G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:06.101    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:06.407    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 23619460 kmers in total.
  0:00:06.408    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:06.840    64M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:06.840    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:06.840    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:06.840    64M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:06.840    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:06.840    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:10.574     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 23619460 kmers
  0:00:10.574     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 23619460 kmers.
  0:00:11.367    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:11.580    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 23286214 kmers in total.
  0:00:11.580    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:12.048    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:12.916    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:13.381    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 10806120 bytes occupied (3.71245 bits per kmer).
  0:00:13.397    88M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:14.675    88M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:14.675    88M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Early tip clipping
  0:00:14.676    88M / 9G    INFO    General                 (construction.cpp          : 253)   Early tip clipper length bound set as (RL - K)
  0:00:14.676    88M / 9G    INFO   Early tip clipping       (early_simplification.hpp  : 181)   Early tip clipping
  0:00:16.978    88M / 9G    INFO   Early tip clipping       (early_simplification.hpp  : 184)   7137863 34-mers were removed by early tip clipper
  0:00:16.979    88M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:16.980    88M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:18.027   124M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 962429 sequences extracted
  0:00:18.593   124M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:18.893   124M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:19.292   348M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:19.293   348M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:19.293   348M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:19.799   372M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 10960640 bytes occupied (3.71241 bits per kmer).
  0:00:19.842   464M / 9G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:21.816   464M / 9G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:22.648   464M / 9G    INFO    General                 (construction.cpp          : 464)   Processed 1924843 edges
  0:00:22.774   312M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 0
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 18
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 19. Coverage mad: 7.413
  0:00:22.774   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:22.799   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:22.869   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:23.131   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:23.776   312M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:24.508   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 18.8784. Fitted coverage std. dev: 5.07148
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.999913
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 4
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 4
  0:00:24.509   308M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4707199
  0:00:24.509   308M / 9G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 18.8784
  0:00:24.509   308M / 9G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 4
  0:00:24.509   308M / 9G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 0
  0:00:24.509   308M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:24.509   308M / 9G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:24.509   308M / 9G    INFO    General                 (graph_simplification.hpp  : 662)   Flanking coverage based disconnection disabled
  0:00:24.509   308M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:24.586   308M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 0 times
  0:00:24.586   308M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:24.586   308M / 9G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:24.586   308M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:24.586   308M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:24.586   308M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:24.729   296M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 915 times
  0:00:24.729   296M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:45.998   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 322286 times
  0:00:45.998   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.005   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 5 times
  0:00:46.005   268M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:00:46.005   268M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.038   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 352 times
  0:00:46.038   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 3 times
  0:00:46.039   244M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.039   244M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.173   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 4132 times
  0:00:46.173   224M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:00:46.173   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.175   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 86 times
  0:00:46.175   224M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.257   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 701 times
  0:00:46.257   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 64 times
  0:00:46.258   216M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.258   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.260   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 7 times
  0:00:46.260   216M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 68 times
  0:00:46.262   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.262   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 22 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 8 times
  0:00:46.266   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 3 times
  0:00:46.266   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.266   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 9 times
  0:00:46.267   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 5 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:46.267   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.267   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.268   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 9 times
  0:00:46.268   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:00:46.268   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.270   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.270   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.313   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 25 times
  0:00:46.313   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:46.318   212M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.318   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:46.319   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:46.319   212M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:00:46.319   212M / 9G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:00:46.319   212M / 9G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:00:46.319   212M / 9G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:00:46.319   212M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:46.319   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.321   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.321   212M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.353   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:46.353   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:46.355   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:46.355   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:46.386   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:46.386   204M / 9G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:00:46.396   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:00:46.398   204M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 11 times
  0:00:46.398   204M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:00:46.402   204M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 21.7425
  0:00:46.402   204M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:00:46.402   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph_with_scaffolds.gfa
  0:00:46.483   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/before_rr.fasta
  0:00:46.579   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph.fastg
  0:00:46.910   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/simplified_contigs.fasta
  0:00:47.002   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/final_contigs.fasta
  0:00:47.097   204M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:00:47.097   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph_with_scaffolds.gfa
  0:00:47.175   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/before_rr.fasta
  0:00:47.272   204M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/assembly_graph.fastg
  0:00:47.608   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/simplified_contigs.fasta
  0:00:47.704   204M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K33/final_contigs.fasta
  0:00:47.807   204M / 9G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:00:47.955    68M / 9G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 0 minutes 47 seconds

== Running assembler: K55

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K55/configs/config.info
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K55/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=55
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  76)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.001     4M / 4M    INFO    General                 (read_converter.hpp        :  59)   Binary reads detected
  0:00:00.001     4M / 4M    INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:00.001     4M / 4M    INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:00.001     4M / 4M    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.002     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:00.002     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:04.658     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:04.658     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:06.935    64M / 9G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:06.935    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:07.293    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28314268 kmers in total.
  0:00:07.293    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:07.877    64M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:07.877    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:07.877    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:07.877    64M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:07.877    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:07.877    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:12.066     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 28314268 kmers
  0:00:12.066     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 28314268 kmers.
  0:00:12.876    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:13.131    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28202227 kmers in total.
  0:00:13.131    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:13.652    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:14.854    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:15.411    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13085528 bytes occupied (3.71191 bits per kmer).
  0:00:15.432    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:16.895    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:16.896    92M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:16.897    92M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:18.486   188M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 1389218 sequences extracted
  0:00:19.394   188M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:19.745   188M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:20.336   516M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:20.336   516M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:20.336   516M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:20.903   524M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13137352 bytes occupied (3.71187 bits per kmer).
  0:00:20.970   636M / 9G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:22.758   636M / 9G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:24.249   636M / 9G    INFO    General                 (construction.cpp          : 464)   Processed 2778430 edges
  0:00:24.444   472M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 0
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 13
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 13. Coverage mad: 5.9304
  0:00:24.444   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:24.456   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:24.487   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:24.595   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:24.841   472M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:25.460   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 32
  0:00:26.235   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 64
  0:00:26.428   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 13.4147. Fitted coverage std. dev: 4.27326
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.999714
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 4
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 4
  0:00:26.429   468M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4788539
  0:00:26.429   468M / 9G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 13.4147
  0:00:26.429   468M / 9G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 4
  0:00:26.429   468M / 9G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 0
  0:00:26.429   468M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:00:26.429   468M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:00:26.429   468M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:26.429   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:26.429   468M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:26.429   468M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.19881 Gb
  0:00:26.429   468M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:00:29.421     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 2778430 edges
  0:00:29.421     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 2778430 sequences.
  0:00:30.192   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:30.427   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28314268 kmers in total.
  0:00:30.427   468M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:30.885   468M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:32.287   488M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:32.894   488M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13137352 bytes occupied (3.71187 bits per kmer).
  0:00:33.194     1G / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:00:34.116     1G / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:00:34.116     1G / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:00:36.204     1G / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:00:36.827     1G / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:00:36.827     1G / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:00:37.296     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:00:40.791     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 42 gaps after checking 620 candidates
  0:00:40.897     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:40.902   480M / 9G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:40.902   480M / 9G    INFO    General                 (graph_simplification.hpp  : 662)   Flanking coverage based disconnection disabled
  0:00:40.902   480M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:41.018   480M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 1 times
  0:00:41.018   480M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:41.018   480M / 9G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:41.019   480M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:41.019   480M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:41.019   480M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:47.765   492M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 538227 times
  0:00:47.765   492M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.261   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 113653 times
  0:01:18.262   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.267  1000M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 2 times
  0:01:18.267  1000M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:01:18.267  1000M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.285   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 558 times
  0:01:18.285   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 6 times
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 4 times
  0:01:18.287   992M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.287   992M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.311   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 789 times
  0:01:18.311   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:01:18.311   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.313   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 102 times
  0:01:18.313   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 108 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 5 times
  0:01:18.342   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 7 times
  0:01:18.342   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.342   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 1 times
  0:01:18.343   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 8 times
  0:01:18.343   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.343   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 18 times
  0:01:18.344   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.344   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 38 times
  0:01:18.346   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.346   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.351   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 76 times
  0:01:18.351   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:01:18.351   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.354   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.354   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.382   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 6 times
  0:01:18.382   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:18.386   988M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:01:18.386   988M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:01:18.386   988M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:01:18.386   988M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:01:18.386   988M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:01:18.386   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:01:18.386   988M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:01:18.386   988M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.18823 Gb
  0:01:18.386   988M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 131072
  0:01:20.765     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 38109 edges
  0:01:20.765     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 38109 sequences.
  0:01:21.696   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:01:21.819   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 5432667 kmers in total.
  0:01:21.819   988M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:01:21.947   988M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:01:22.072  1000M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:01:22.177  1000M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 2527456 bytes occupied (3.72186 bits per kmer).
  0:01:22.316     1G / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:01:22.439     1G / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:01:22.439     1G / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:01:22.466     1G / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:01:24.538     1G / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:01:24.538     1G / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:01:24.543     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:01:24.588     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 0 gaps after checking 24 candidates
  0:01:24.591     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:01:24.591     1G / 9G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:01:24.591     1G / 9G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:01:24.591     1G / 9G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:01:24.591     1G / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:01:24.591     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:24.595     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:24.595     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:24.615     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:01:24.615     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:01:24.618     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:01:24.618     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:01:24.636     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:01:24.636     1G / 9G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:01:24.651     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:01:25.067     1G / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 6674 times
  0:01:25.067     1G / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:25.078     1G / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 14.9594
  0:01:25.078     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:25.078     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph_with_scaffolds.gfa
  0:01:25.153     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/before_rr.fasta
  0:01:25.235     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph.fastg
  0:01:25.528     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/simplified_contigs.fasta
  0:01:25.610     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/final_contigs.fasta
  0:01:25.690     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:25.690     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph_with_scaffolds.gfa
  0:01:25.766     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/before_rr.fasta
  0:01:25.848     1G / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/assembly_graph.fastg
  0:01:26.140     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/simplified_contigs.fasta
  0:01:26.225     1G / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K55/final_contigs.fasta
  0:01:26.312     1G / 9G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:01:31.344    72M / 9G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 1 minutes 31 seconds

== Running assembler: K77

  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K77/configs/config.info
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  74)   Loaded config from /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/K77/configs/careful_mode.info
  0:00:00.001     4M / 4M    INFO    General                 (memory_limit.cpp          :  49)   Memory limit set to 250 Gb
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  87)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  88)   Maximum k-mer length: 128
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  89)   Assembling dataset (/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/dataset.info) with K=77
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  90)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  51)   SPAdes started
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  58)   Starting from stage: construction
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  65)   Two-step RR enabled: 0
  0:00:00.001     4M / 4M    INFO    General                 (launch.hpp                :  76)   Will need read mapping, kmer mapper will be attached
  0:00:00.001     4M / 4M    INFO   StageManager             (stage.cpp                 : 132)   STAGE == de Bruijn graph construction
  0:00:00.002     4M / 4M    INFO    General                 (read_converter.hpp        :  59)   Binary reads detected
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 111)   Max read length 151
  0:00:00.002     4M / 4M    INFO    General                 (construction.cpp          : 117)   Average read length 151
  0:00:00.002     4M / 4M    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == k+1-mer counting
  0:00:00.002     4M / 4M    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:00.002     4M / 4M    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20825 Gb
  0:00:00.002     4M / 4M    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:05.302     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 289)   Processed 1850120 reads
  0:00:05.302     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 295)   Adding contigs from previous K
  0:00:07.111    64M / 9G    INFO    General                 (kmer_splitters.hpp        : 308)   Used 1850120 reads
  0:00:07.111    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:08.494    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28724894 kmers in total.
  0:00:08.494    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:09.412    64M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Extension index construction
  0:00:09.412    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:09.412    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:09.412    64M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:09.412    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20703 Gb
  0:00:09.412    64M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:14.039     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 380)   Processed 28724894 kmers
  0:00:14.039     8G / 9G    INFO    General                 (kmer_splitters.hpp        : 385)   Used 28724894 kmers.
  0:00:14.810    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:15.275    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28787624 kmers in total.
  0:00:15.275    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:16.031    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:17.075    64M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:18.029    64M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13356976 bytes occupied (3.71187 bits per kmer).
  0:00:18.052    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build:  99)   Building k-mer extensions from k+1-mers
  0:00:19.604    92M / 9G    INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 103)   Building k-mer extensions from k+1-mers finished.
  0:00:19.605    92M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Condensing graph
  0:00:19.607    92M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 355)   Extracting unbranching paths
  0:00:21.398   192M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 374)   Extracting unbranching paths finished. 1160163 sequences extracted
  0:00:22.400   192M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 310)   Collecting perfect loops
  0:00:22.759   192M / 9G    INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 343)   Collecting perfect loops finished. 0 loops collected
  0:00:23.348   464M / 9G    INFO    General                 (stage.cpp                 : 101)   PROCEDURE == Filling coverage indices (PHM)
  0:00:23.348   464M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:23.348   464M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:24.158   468M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13327808 bytes occupied (3.71185 bits per kmer).
  0:00:24.220   580M / 9G    INFO    General                 (construction.cpp          : 388)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:25.615   580M / 9G    INFO    General                 (construction.cpp          : 508)   Filling coverage and flanking coverage from PHM
  0:00:27.014   580M / 9G    INFO    General                 (construction.cpp          : 464)   Processed 2320325 edges
  0:00:27.222   428M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == EC Threshold Finding
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 181)   Kmer coverage valley at: 2
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 201)   K-mer histogram maximum: 8
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 237)   Estimated median coverage: 9. Coverage mad: 4.4478
  0:00:27.222   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 259)   Fitting coverage model
  0:00:27.231   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 2
  0:00:27.252   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 4
  0:00:27.323   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 8
  0:00:27.472   428M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 16
  0:00:27.697   424M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 295)   ... iteration 32
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 309)   Fitted mean coverage: 9.19109. Fitted coverage std. dev: 3.34463
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 334)   Probability of erroneous kmer at valley: 0.354172
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 358)   Preliminary threshold calculated as: 5
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 362)   Threshold adjusted to: 5
  0:00:27.802   420M / 9G    INFO    General                 (kmer_coverage_model.cpp   : 375)   Estimated genome size (ignoring repeats): 4449079
  0:00:27.802   420M / 9G    INFO    General                 (genomic_info_filler.cpp   : 112)   Mean coverage was calculated as 9.19109
  0:00:27.802   420M / 9G    INFO    General                 (genomic_info_filler.cpp   : 127)   EC coverage threshold value was calculated as 5
  0:00:27.802   420M / 9G    INFO    General                 (genomic_info_filler.cpp   : 128)   Trusted kmer low bound: 1
  0:00:27.802   420M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:00:27.802   420M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:00:27.802   420M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:27.802   420M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:27.802   420M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:27.802   420M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.19979 Gb
  0:00:27.802   420M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:31.220     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 2320325 edges
  0:00:31.220     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 2320325 sequences.
  0:00:31.904   416M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:32.333   416M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 28724894 kmers in total.
  0:00:32.333   416M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:33.009   416M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:34.197   440M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:35.166   440M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 13327808 bytes occupied (3.71185 bits per kmer).
  0:00:35.435     1G / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:00:36.291     1G / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:00:36.292     1G / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:00:38.167     1G / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:00:38.744     1G / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:00:38.744     1G / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:00:39.262     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:00:42.495     1G / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 82 gaps after checking 1106 candidates
  0:00:42.691     1G / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Raw Simplification
  0:00:42.697   432M / 9G    INFO    General                 (simplification.cpp        : 128)   PROCEDURE == InitialCleaning
  0:00:42.697   432M / 9G    INFO    General                 (simplification.cpp        :  62)   Most init cleaning disabled on main iteration
  0:00:42.697   432M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Self conjugate edge remover
  0:00:42.797   432M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Self conjugate edge remover triggered 0 times
  0:00:42.797   432M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification
  0:00:42.797   432M / 9G    INFO    General                 (simplification.cpp        : 357)   Graph simplification started
  0:00:42.797   432M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:42.797   432M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 1
  0:00:42.797   432M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:51.729   380M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 551441 times
  0:00:51.729   380M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.255   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1919 times
  0:00:52.255   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.276   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:52.276   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 2
  0:00:52.276   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 12 times
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.277   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.280   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 94 times
  0:00:52.280   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 3
  0:00:52.280   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.282   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 60 times
  0:00:52.282   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 9 times
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 3 times
  0:00:52.286   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 4
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:52.286   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 18 times
  0:00:52.287   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 5
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.287   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.288   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:52.288   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.291   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 85 times
  0:00:52.291   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 6
  0:00:52.291   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.291   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.292   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.292   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.292   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 257 times
  0:00:52.305   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 7
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.305   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 443 times
  0:00:52.329   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 8
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 1 times
  0:00:52.329   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 607 times
  0:00:52.363   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 9
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.363   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 572 times
  0:00:52.398   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 10
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.398   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.438   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 503 times
  0:00:52.438   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 11
  0:00:52.438   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.455   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 1 times
  0:00:52.455   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.481   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.481   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:52.496   392M / 9G    INFO    General                 (simplification.cpp        : 362)   PROCEDURE == Simplification cycle, iteration 12
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Low coverage edge remover
  0:00:52.496   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Low coverage edge remover triggered 0 times
  0:00:52.496   392M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Gap Closer
  0:00:52.496   392M / 9G    INFO    General                 (graph_pack.hpp            : 101)   Index refill
  0:00:52.497   392M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 301)   Building kmer index
  0:00:52.497   392M / 9G    INFO    General                 (kmer_index_builder.hpp    : 117)   Splitting kmer instances into 256 files using 16 threads. This might take a while.
  0:00:52.497   392M / 9G    INFO    General                 (file_limit.hpp            :  32)   Open file limit set to 1024
  0:00:52.497   392M / 9G    INFO    General                 (kmer_splitters.hpp        :  89)   Memory available for splitting buffers: 5.20036 Gb
  0:00:52.497   392M / 9G    INFO    General                 (kmer_splitters.hpp        :  97)   Using cell size of 87381
  0:00:55.146     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  77)   Processed 142399 edges
  0:00:55.146     9G / 9G    INFO    General                 (edge_index_builders.hpp   :  82)   Used 142399 sequences.
  0:00:55.840   388M / 9G    INFO    General                 (kmer_index_builder.hpp    : 120)   Starting k-mer counting.
  0:00:56.003   388M / 9G    INFO    General                 (kmer_index_builder.hpp    : 127)   K-mer counting done. There are 9706450 kmers in total.
  0:00:56.003   388M / 9G    INFO    General                 (kmer_index_builder.hpp    : 133)   Merging temporary buckets.
  0:00:56.238   388M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 314)   Building perfect hash indices
  0:00:56.487   392M / 9G    INFO    General                 (kmer_index_builder.hpp    : 150)   Merging final buckets.
  0:00:56.792   392M / 9G    INFO   K-mer Index Building     (kmer_index_builder.hpp    : 336)   Index built. Total 4508952 bytes occupied (3.71625 bits per kmer).
  0:00:57.029   616M / 9G    INFO    General                 (edge_index_builders.hpp   : 107)   Collecting edge information from graph, this takes a while.
  0:00:57.304   616M / 9G    INFO    General                 (edge_index.hpp            :  92)   Index refilled
  0:00:57.305   616M / 9G    INFO    General                 (gap_closer.cpp            : 159)   Preparing shift maps
  0:00:57.515   636M / 9G    INFO    General                 (gap_closer.cpp            : 119)   Processing paired reads (takes a while)
  0:00:58.964   636M / 9G    INFO    General                 (gap_closer.cpp            : 138)   Used 462530 paired reads
  0:00:58.964   636M / 9G    INFO    General                 (gap_closer.cpp            : 140)   Merging paired indices
  0:00:59.042   616M / 9G    INFO   GapCloser                (gap_closer.cpp            : 346)   Closing short gaps
  0:00:59.203   616M / 9G    INFO   GapCloser                (gap_closer.cpp            : 380)   Closing short gaps complete: filled 1 gaps after checking 181 candidates
  0:00:59.242   616M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Simplification Cleanup
  0:00:59.242   616M / 9G    INFO    General                 (simplification.cpp        : 196)   PROCEDURE == Post simplification
  0:00:59.242   616M / 9G    INFO    General                 (graph_simplification.hpp  : 453)   Disconnection of relatively low covered edges disabled
  0:00:59.242   616M / 9G    INFO    General                 (graph_simplification.hpp  : 489)   Complex tip clipping disabled
  0:00:59.242   616M / 9G    INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:59.242   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.273   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:59.273   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:59.297   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:59.297   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Tip clipper
  0:00:59.314   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Tip clipper triggered 0 times
  0:00:59.314   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Bulge remover
  0:00:59.335   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Bulge remover triggered 0 times
  0:00:59.335   616M / 9G    INFO    General                 (simplification.cpp        : 330)   Disrupting self-conjugate edges
  0:00:59.432   616M / 9G    INFO   Simplification           (parallel_processing.hpp   : 165)   Running Removing isolated edges
  0:01:03.531   392M / 9G    INFO   Simplification           (parallel_processing.hpp   : 167)   Removing isolated edges triggered 68071 times
  0:01:03.531   392M / 9G    INFO    General                 (simplification.cpp        : 340)   Removing all the edges having coverage 1 and less
  0:01:03.532   392M / 9G    INFO    General                 (simplification.cpp        : 470)   Counting average coverage
  0:01:03.533   392M / 9G    INFO    General                 (simplification.cpp        : 476)   Average coverage = 9.393
  0:01:03.533   392M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Mismatch Correction
  0:01:03.533   392M / 9G    INFO    General                 (graph_pack.hpp            : 109)   Normalizing k-mer map. Total 311881 kmers to process
  0:01:03.724   388M / 9G    INFO    General                 (graph_pack.hpp            : 111)   Normalizing done
  0:01:06.678   400M / 9G    INFO    General                 (mismatch_shall_not_pass.hp: 189)   Finished collecting potential mismatches positions
  0:01:06.774   388M / 9G    INFO    General                 (mismatch_shall_not_pass.hp: 290)   All edges processed
  0:01:06.775   388M / 9G    INFO    General                 (mismatch_correction.cpp   :  27)   Corrected 0 nucleotides
  0:01:06.776   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:06.776   388M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph_with_scaffolds.gfa
  0:01:06.838   388M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/before_rr.fasta
  0:01:06.900   388M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph.fastg
  0:01:07.127   388M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/simplified_contigs.fasta
  0:01:07.203   388M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/intermediate_contigs.fasta
  0:01:07.279   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Paired Information Counting
  0:01:07.292   388M / 9G    INFO    General                 (graph_pack.hpp            : 109)   Normalizing k-mer map. Total 311881 kmers to process
  0:01:07.292   388M / 9G    INFO    General                 (graph_pack.hpp            : 111)   Normalizing done
  0:01:07.293   388M / 9G    INFO    General                 (pair_info_count.cpp       : 320)   Min edge length for estimation: 6989
  0:01:07.293   388M / 9G    INFO    General                 (pair_info_count.cpp       : 331)   Estimating insert size for library #0
  0:01:07.293   388M / 9G    INFO    General                 (pair_info_count.cpp       : 190)   Estimating insert size (takes a while)
  0:01:07.397   660M / 9G    INFO    General                 (pair_info_count.cpp       :  39)   Selecting usual mapper
  0:01:09.274   660M / 9G    INFO    General                 (sequence_mapper_notifier.h:  98)   Total 462530 reads processed
  0:01:10.663   660M / 9G    INFO    General                 (pair_info_count.cpp       : 209)   Edge pairs: 67108864 (rough upper limit)
  0:01:10.663   660M / 9G    INFO    General                 (pair_info_count.cpp       : 213)   189193 paired reads (40.9039% of all) aligned to long edges
  0:01:10.665   388M / 9G    INFO    General                 (pair_info_count.cpp       : 354)     Insert size = 300.004, deviation = 29.9794, left quantile = 262, right quantile = 338, read length = 151
  0:01:10.730   580M / 9G    INFO    General                 (pair_info_count.cpp       : 371)   Filtering data for library #0
  0:01:10.730   580M / 9G    INFO    General                 (pair_info_count.cpp       :  39)   Selecting usual mapper
  0:01:12.298   580M / 9G    INFO    General                 (sequence_mapper_notifier.h:  98)   Total 462530 reads processed
  0:01:12.298   580M / 9G    INFO    General                 (pair_info_count.cpp       : 383)   Mapping library #0
  0:01:12.298   580M / 9G    INFO    General                 (pair_info_count.cpp       : 385)   Mapping paired reads (takes a while)
  0:01:12.298   580M / 9G    INFO    General                 (pair_info_count.cpp       : 289)   Left insert size quantile 262, right insert size quantile 338, filtering threshold 2, rounding threshold 0
  0:01:12.310   592M / 9G    INFO    General                 (pair_info_count.cpp       :  39)   Selecting usual mapper
  0:01:13.865   592M / 9G    INFO    General                 (sequence_mapper_notifier.h:  98)   Total 462530 reads processed
  0:01:13.877   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Distance Estimation
  0:01:13.877   388M / 9G    INFO    General                 (distance_estimation.cpp   : 173)   Processing library #0
  0:01:13.877   388M / 9G    INFO    General                 (distance_estimation.cpp   : 149)   Weight Filter Done
  0:01:13.877   388M / 9G    INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:01:13.910   388M / 9G    INFO    General                 (distance_estimation.cpp   :  34)   Filtering info
  0:01:13.910   388M / 9G    INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; index size: 17495
  0:01:13.921   392M / 9G    INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering
  0:01:13.921   388M / 9G    INFO    General                 (distance_estimation.cpp   : 156)   Refining clustered pair information
  0:01:13.927   388M / 9G    INFO    General                 (distance_estimation.cpp   : 158)   The refining of clustered pair information has been finished
  0:01:13.927   388M / 9G    INFO    General                 (distance_estimation.cpp   : 160)   Improving paired information
  0:01:13.947   388M / 9G    INFO   PairInfoImprover         (pair_info_improver.hpp    : 103)   Paired info stats: missing = 620; contradictional = 628
  0:01:13.967   388M / 9G    INFO   PairInfoImprover         (pair_info_improver.hpp    : 103)   Paired info stats: missing = 33; contradictional = 0
  0:01:13.967   388M / 9G    INFO    General                 (distance_estimation.cpp   : 103)   Filling scaffolding index
  0:01:13.967   388M / 9G    INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SMOOTHING distance estimator
  0:01:13.971   388M / 9G    INFO    General                 (distance_estimation.cpp   :  34)   Filtering info
  0:01:13.971   388M / 9G    INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; index size: 6265
  0:01:13.974   388M / 9G    INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering
  0:01:13.974   388M / 9G    INFO    General                 (distance_estimation.cpp   : 182)   Clearing raw paired index
  0:01:13.977   388M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Repeat Resolving
  0:01:13.977   388M / 9G    INFO    General                 (repeat_resolving.cpp      :  69)   Using Path-Extend repeat resolving
  0:01:13.977   388M / 9G    INFO    General                 (launcher.cpp              : 477)   ExSPAnder repeat resolving tool started
  0:01:13.992   400M / 9G    INFO    General                 (launcher.cpp              : 392)   Creating main extenders, unique edge length = 2000
  0:01:13.992   400M / 9G    INFO    General                 (extenders_logic.cpp       : 275)   Estimated coverage of library #0 is 9.393
  0:01:13.993   400M / 9G    INFO    General                 (extenders_logic.cpp       : 275)   Estimated coverage of library #0 is 9.393
  0:01:13.994   400M / 9G    INFO    General                 (extenders_logic.cpp       : 472)   Using 1 paired-end library
  0:01:13.994   400M / 9G    INFO    General                 (extenders_logic.cpp       : 473)   Using 1 paired-end scaffolding library
  0:01:13.994   400M / 9G    INFO    General                 (extenders_logic.cpp       : 474)   Using 0 single read libraries
  0:01:13.994   400M / 9G    INFO    General                 (launcher.cpp              : 420)   Total number of extenders is 3
  0:01:13.994   400M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 0 paths from 3082 (0%)
  0:01:14.011   400M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 128 paths from 3082 (4%)
  0:01:14.022   404M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 256 paths from 3082 (8%)
  0:01:14.027   404M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 309 paths from 3082 (10%)
  0:01:14.052   404M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 512 paths from 3082 (16%)
  0:01:14.066   404M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 618 paths from 3082 (20%)
  0:01:14.107   408M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 927 paths from 3082 (30%)
  0:01:14.114   408M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 1024 paths from 3082 (33%)
  0:01:14.153   412M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 1236 paths from 3082 (40%)
  0:01:14.229   416M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 1545 paths from 3082 (50%)
  0:01:14.299   416M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 1854 paths from 3082 (60%)
  0:01:14.343   420M / 9G    INFO    General                 (path_extender.hpp         : 883)   Processed 2048 paths from 3082 (66%)
  0:01:14.365   420M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 2163 paths from 3082 (70%)
  0:01:14.432   424M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 2472 paths from 3082 (80%)
  0:01:14.508   428M / 9G    INFO    General                 (path_extender.hpp         : 885)   Processed 2781 paths from 3082 (90%)
  0:01:14.532   428M / 9G    INFO    General                 (launcher.cpp              : 234)   Finalizing paths
  0:01:14.532   428M / 9G    INFO    General                 (launcher.cpp              : 236)   Deduplicating paths
  0:01:14.546   420M / 9G    INFO    General                 (launcher.cpp              : 240)   Paths deduplicated
  0:01:14.546   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 295)   Removing overlaps
  0:01:14.546   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 298)   Sorting paths
  0:01:14.546   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 305)   Marking overlaps
  0:01:14.546   420M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 130)   Marking start/end overlaps
  0:01:14.549   420M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 133)   Marking remaining overlaps
  0:01:14.551   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 308)   Splitting paths
  0:01:14.554   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 313)   Deduplicating paths
  0:01:14.557   420M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 315)   Overlaps removed
  0:01:14.561   420M / 9G    INFO    General                 (launcher.cpp              : 257)   Paths finalized
  0:01:14.561   420M / 9G    INFO    General                 (launcher.cpp              : 427)   Closing gaps in paths
  0:01:14.568   424M / 9G    INFO    General                 (launcher.cpp              : 455)   Gap closing completed
  0:01:14.570   424M / 9G    INFO    General                 (launcher.cpp              : 286)   Traversing tandem repeats
  0:01:14.594   424M / 9G    INFO    General                 (launcher.cpp              : 296)   Traversed 549 loops
  0:01:14.594   424M / 9G    INFO    General                 (launcher.cpp              : 234)   Finalizing paths
  0:01:14.594   424M / 9G    INFO    General                 (launcher.cpp              : 236)   Deduplicating paths
  0:01:14.595   424M / 9G    INFO    General                 (launcher.cpp              : 240)   Paths deduplicated
  0:01:14.595   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 295)   Removing overlaps
  0:01:14.595   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 298)   Sorting paths
  0:01:14.596   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 305)   Marking overlaps
  0:01:14.596   424M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 130)   Marking start/end overlaps
  0:01:14.597   424M / 9G    INFO   OverlapRemover           (pe_resolver.hpp           : 133)   Marking remaining overlaps
  0:01:14.598   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 308)   Splitting paths
  0:01:14.599   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 313)   Deduplicating paths
  0:01:14.599   424M / 9G    INFO   PEResolver               (pe_resolver.hpp           : 315)   Overlaps removed
  0:01:14.601   424M / 9G    INFO    General                 (launcher.cpp              : 257)   Paths finalized
  0:01:14.604   424M / 9G    INFO    General                 (launcher.cpp              : 529)   ExSPAnder repeat resolving tool finished
  0:01:14.625   400M / 9G    INFO   StageManager             (stage.cpp                 : 132)   STAGE == Contig Output
  0:01:14.625   400M / 9G    INFO    General                 (contig_output_stage.cpp   :  40)   Writing GFA to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph_with_scaffolds.gfa
  0:01:14.676   400M / 9G    INFO    General                 (contig_output.hpp         :  22)   Outputting contigs to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/before_rr.fasta
  0:01:14.739   400M / 9G    INFO    General                 (contig_output_stage.cpp   :  51)   Outputting FastG graph to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/assembly_graph.fastg
  0:01:14.954   404M / 9G    INFO    General                 (contig_output_stage.cpp   :  20)   Outputting FastG paths to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/final_contigs.paths
  0:01:15.046   400M / 9G    INFO    General                 (contig_output_stage.cpp   :  20)   Outputting FastG paths to /home/annotest/AssemblyWS/SPAdes/SPAdes_Out//K77/scaffolds.paths
  0:01:15.116   400M / 9G    INFO    General                 (launch.hpp                : 149)   SPAdes finished
  0:01:15.296    68M / 9G    INFO    General                 (main.cpp                  : 109)   Assembling time: 0 hours 1 minutes 15 seconds

===== Assembling finished. Used k-mer sizes: 21, 33, 55, 77 


===== Mismatch correction started.

== Processing of scaffolds


== Running contig polishing tool: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-corrector-core /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/scaffolds/configs/corrector.info /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta


== Dataset description file was created: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/scaffolds/configs/corrector.info

/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/scaffolds/configs/log.properties  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  58)   Starting MismatchCorrector, built from N/A, git revision N/A
  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  59)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.000     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 195)   Splitting assembly...
  0:00:00.000     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 196)   Assembly file: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta
  0:00:00.174     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 203)   Processing paired sublib of number 0
  0:00:00.174     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 206)   /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
  0:00:00.174     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 140)   Running bwa index ...: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta
[bwa_index] Pack FASTA... 0.07 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.31 seconds elapse.
[bwa_index] Update BWT... 0.06 sec
[bwa_index] Pack forward-only FASTA... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 0.75 sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta
[main] Real time: 2.265 sec; CPU: 2.259 sec
  0:00:02.442     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 149)   Running bwa mem ...:/home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem  -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz  > /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_o5hhdch0/lib0_VA0t3N/tmp.sam
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_scaffolds.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
[main] Real time: 9.495 sec; CPU: 87.977 sec
  0:00:11.999     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 209)   Adding samfile /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_o5hhdch0/lib0_VA0t3N/tmp.sam
  0:00:15.975    60M / 60M   INFO   DatasetProcessor         (dataset_processor.cpp     : 105)   processed 1000000reads, flushing
  0:00:16.183    20M / 60M   INFO   DatasetProcessor         (dataset_processor.cpp     : 235)   Processing contigs
  0:00:17.116   260M / 264M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_16_length_68666_cov_9.322297 processed with 27 changes in thread 11
  0:00:17.186   280M / 284M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_15_length_75367_cov_9.330734 processed with 31 changes in thread 14
  0:00:17.203   284M / 284M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_14_length_79082_cov_9.256731 processed with 30 changes in thread 10
  0:00:17.266   288M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_12_length_80943_cov_9.156667 processed with 47 changes in thread 5
  0:00:17.277   284M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_13_length_79621_cov_9.427487 processed with 22 changes in thread 3
  0:00:17.321   280M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_11_length_86382_cov_9.255362 processed with 41 changes in thread 13
  0:00:17.327   268M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_10_length_91841_cov_9.187971 processed with 40 changes in thread 0
  0:00:17.444   276M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_9_length_93568_cov_9.157053 processed with 61 changes in thread 4
  0:00:17.531   272M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_8_length_102123_cov_9.304206 processed with 45 changes in thread 15
  0:00:17.564   264M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_5_length_105317_cov_9.323489 processed with 53 changes in thread 1
  0:00:17.568   260M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_6_length_103454_cov_9.340192 processed with 46 changes in thread 7
  0:00:17.638   248M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_7_length_103373_cov_9.283738 processed with 42 changes in thread 2
  0:00:17.713   240M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_4_length_117049_cov_9.316383 processed with 56 changes in thread 9
  0:00:17.840   232M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_3_length_127286_cov_9.299499 processed with 56 changes in thread 8
  0:00:17.860   220M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_17_length_67221_cov_9.148710 processed with 42 changes in thread 11
  0:00:17.918   216M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_19_length_59516_cov_9.118121 processed with 41 changes in thread 10
  0:00:17.949   212M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_21_length_58500_cov_9.342707 processed with 40 changes in thread 3
  0:00:17.953   208M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_20_length_59353_cov_9.146029 processed with 45 changes in thread 5
  0:00:17.965   204M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_2_length_140662_cov_9.276381 processed with 60 changes in thread 12
  0:00:17.965   204M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_22_length_56255_cov_9.120474 processed with 32 changes in thread 13
  0:00:17.974   188M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_1_length_142002_cov_9.288807 processed with 83 changes in thread 6
  0:00:17.976   188M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_23_length_54525_cov_9.206270 processed with 20 changes in thread 0
  0:00:18.097   168M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_18_length_61016_cov_9.145982 processed with 36 changes in thread 14
  0:00:18.153   164M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_25_length_53628_cov_9.122052 processed with 46 changes in thread 15
  0:00:18.172   160M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_26_length_52671_cov_8.958684 processed with 29 changes in thread 1
  0:00:18.195   156M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_24_length_54285_cov_9.341924 processed with 32 changes in thread 4
  0:00:18.231   152M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_28_length_49923_cov_9.205292 processed with 32 changes in thread 2
  0:00:18.272   152M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_27_length_51962_cov_9.223783 processed with 15 changes in thread 7
  0:00:18.303   148M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_29_length_49269_cov_9.104692 processed with 32 changes in thread 9
  0:00:18.412   144M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_32_length_44267_cov_9.305386 processed with 17 changes in thread 10
  0:00:18.426   144M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_30_length_46027_cov_9.221349 processed with 19 changes in thread 8
  0:00:18.444   140M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_34_length_42977_cov_9.193357 processed with 25 changes in thread 5
  0:00:18.450   140M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_31_length_45461_cov_9.278821 processed with 20 changes in thread 11
  0:00:18.452   136M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_38_length_40177_cov_9.005012 processed with 20 changes in thread 6
  0:00:18.452   132M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_37_length_40871_cov_9.215571 processed with 14 changes in thread 0
  0:00:18.459   128M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_33_length_42997_cov_9.426375 processed with 14 changes in thread 3
  0:00:18.461   128M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_36_length_42333_cov_9.380561 processed with 13 changes in thread 12
  0:00:18.462   120M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_35_length_42826_cov_9.105312 processed with 29 changes in thread 13
  0:00:18.578   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_39_length_39763_cov_9.213929 processed with 21 changes in thread 14
  0:00:18.611   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_42_length_36235_cov_9.288484 processed with 27 changes in thread 4
  0:00:18.619   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_40_length_39706_cov_9.178480 processed with 28 changes in thread 15
  0:00:18.631   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_41_length_39340_cov_9.266689 processed with 10 changes in thread 1
  0:00:18.683   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_44_length_35354_cov_9.258951 processed with 15 changes in thread 7
  0:00:18.687   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_43_length_35960_cov_9.286542 processed with 11 changes in thread 2
  0:00:18.717   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_45_length_35098_cov_9.382456 processed with 7 changes in thread 9
  0:00:18.762   112M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_54_length_27094_cov_9.077100 processed with 9 changes in thread 13
  0:00:18.791   108M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_53_length_28791_cov_9.096399 processed with 12 changes in thread 12
  0:00:18.797   104M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_52_length_29416_cov_8.992501 processed with 26 changes in thread 3
  0:00:18.802   100M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_46_length_34659_cov_9.288271 processed with 17 changes in thread 10
  0:00:18.821    96M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_50_length_31620_cov_9.175221 processed with 20 changes in thread 0
  0:00:18.824    96M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_48_length_32089_cov_9.280301 processed with 21 changes in thread 5
  0:00:18.869    92M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_55_length_26224_cov_9.265537 processed with 12 changes in thread 14
  0:00:18.879    92M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_47_length_32658_cov_9.352353 processed with 15 changes in thread 8
  0:00:18.887    88M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_49_length_31943_cov_9.358972 processed with 18 changes in thread 11
  0:00:18.908    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_51_length_31299_cov_9.338928 processed with 17 changes in thread 6
  0:00:18.913    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_56_length_26007_cov_9.247358 processed with 13 changes in thread 4
  0:00:18.916    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_57_length_24953_cov_9.437128 processed with 17 changes in thread 15
  0:00:18.917    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_58_length_24791_cov_9.431820 processed with 5 changes in thread 1
  0:00:18.956    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_60_length_24062_cov_9.420930 processed with 7 changes in thread 2
  0:00:18.974    84M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_59_length_24346_cov_9.340517 processed with 6 changes in thread 7
  0:00:18.985    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_61_length_23950_cov_9.240355 processed with 14 changes in thread 9
  0:00:19.034    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_62_length_23365_cov_9.311276 processed with 3 changes in thread 13
  0:00:19.055    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_65_length_22151_cov_9.331974 processed with 4 changes in thread 10
  0:00:19.060    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_63_length_23326_cov_9.087402 processed with 7 changes in thread 12
  0:00:19.061    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_64_length_22851_cov_9.505225 processed with 13 changes in thread 3
  0:00:19.063    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_67_length_21459_cov_9.305631 processed with 9 changes in thread 5
  0:00:19.072    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_66_length_21630_cov_9.460168 processed with 7 changes in thread 0
  0:00:19.114    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_70_length_20349_cov_9.175069 processed with 15 changes in thread 11
  0:00:19.115    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_68_length_21372_cov_9.361446 processed with 4 changes in thread 14
  0:00:19.128    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_69_length_20560_cov_8.885710 processed with 20 changes in thread 8
  0:00:19.154    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_72_length_20049_cov_9.416383 processed with 1 changes in thread 4
  0:00:19.193    80M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_71_length_20334_cov_9.237153 processed with 18 changes in thread 6
  0:00:19.849    76M / 288M  INFO   DatasetProcessor         (dataset_processor.cpp     : 255)   Gluing processed contigs
  0:00:19.870    64M / 288M  INFO    General                 (main.cpp                  :  72)   Correcting time: 0 hours 0 minutes 19 seconds

== Processing of contigs


== Running contig polishing tool: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-corrector-core /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/contigs/configs/corrector.info /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta


== Dataset description file was created: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/contigs/configs/corrector.info

/home/annotest/AssemblyWS/SPAdes/SPAdes_Out/mismatch_corrector/contigs/configs/log.properties  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  :  58)   Starting MismatchCorrector, built from N/A, git revision N/A
  0:00:00.001     4M / 4M    INFO    General                 (main.cpp                  :  59)   Maximum # of threads to use (adjusted due to OMP capabilities): 16
  0:00:00.001     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 195)   Splitting assembly...
  0:00:00.001     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 196)   Assembly file: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta
  0:00:00.261     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 203)   Processing paired sublib of number 0
  0:00:00.261     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 206)   /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
  0:00:00.261     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 140)   Running bwa index ...: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta
[bwa_index] Pack FASTA... 0.07 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.40 seconds elapse.
[bwa_index] Update BWT... 0.06 sec
[bwa_index] Pack forward-only FASTA... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 0.76 sec
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa index -a is /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta
[main] Real time: 2.360 sec; CPU: 2.351 sec
  0:00:02.625     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 149)   Running bwa mem ...:/home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem  -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz  > /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_ts3eej1f/lib0_xpD8b2/tmp.sam
[main] Version: 0.7.12-r1039
[main] CMD: /home/share/apps/SPAdes-3.12.0-Linux/bin/spades-bwa mem -v 1 -t 16 /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/misc/assembled_contigs.fasta /home/annotest/AssemblyWS/SPAdes/cabV2_read1.fq.gz /home/annotest/AssemblyWS/SPAdes/cabV2_read2.fq.gz
[main] Real time: 9.463 sec; CPU: 90.052 sec
  0:00:12.146     4M / 4M    INFO   DatasetProcessor         (dataset_processor.cpp     : 209)   Adding samfile /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/tmp/corrector_ts3eej1f/lib0_xpD8b2/tmp.sam
  0:00:15.640    56M / 56M   INFO   DatasetProcessor         (dataset_processor.cpp     : 105)   processed 1000000reads, flushing
  0:00:16.517    20M / 60M   INFO   DatasetProcessor         (dataset_processor.cpp     : 235)   Processing contigs
  0:00:16.820    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_16_length_20142_cov_9.388886 processed with 8 changes in thread 11
  0:00:16.825    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_15_length_20345_cov_9.764210 processed with 0 changes in thread 15
  0:00:16.832    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_11_length_22641_cov_9.907818 processed with 0 changes in thread 2
  0:00:16.832    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_14_length_21372_cov_9.361446 processed with 4 changes in thread 3
  0:00:16.841    88M / 88M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_13_length_21930_cov_9.955384 processed with 1 changes in thread 7
  0:00:16.850    92M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_6_length_24310_cov_9.351917 processed with 6 changes in thread 1
  0:00:16.857    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_8_length_24220_cov_9.404962 processed with 5 changes in thread 4
  0:00:16.864    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_12_length_22151_cov_9.331974 processed with 3 changes in thread 14
  0:00:16.869    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_9_length_23745_cov_9.673187 processed with 5 changes in thread 5
  0:00:16.873    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_10_length_23680_cov_9.427319 processed with 6 changes in thread 8
  0:00:16.874    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_2_length_28101_cov_9.624358 processed with 7 changes in thread 0
  0:00:16.881    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_7_length_24297_cov_9.539595 processed with 6 changes in thread 13
  0:00:16.892    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_5_length_26093_cov_9.203990 processed with 6 changes in thread 6
  0:00:16.900    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_3_length_27449_cov_9.297348 processed with 4 changes in thread 9
  0:00:16.910    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_4_length_27046_cov_9.518818 processed with 5 changes in thread 10
  0:00:16.977    88M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_1_length_31311_cov_9.432349 processed with 0 changes in thread 12
  0:00:17.085    84M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_17_length_20131_cov_9.570460 processed with 1 changes in thread 11
  0:00:17.105    80M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 251)   Contig NODE_18_length_20049_cov_9.416383 processed with 1 changes in thread 15
  0:00:20.082    80M / 92M   INFO   DatasetProcessor         (dataset_processor.cpp     : 255)   Gluing processed contigs
  0:00:20.109    64M / 92M   INFO    General                 (main.cpp                  :  72)   Correcting time: 0 hours 0 minutes 20 seconds

===== Mismatch correction finished.

 * Assembled contigs are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/contigs.fasta
 * Assembled scaffolds are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/scaffolds.fasta
 * Assembly graph is in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/assembly_graph.fastg
 * Assembly graph in GFA format is in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/assembly_graph_with_scaffolds.gfa
 * Paths in the assembly graph corresponding to the contigs are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/scaffolds.paths

======= SPAdes pipeline finished.

SPAdes log can be found here: /home/annotest/AssemblyWS/SPAdes/SPAdes_Out/spades.log

Thank you for using SPAdes!

    -Use 16 CPU threads

    -Output is saved in SPAdes_Out directory

    MaSuRCA assembler

    • Create directory for running MaSuRCA
    In [79]:
    cd ..

    /home/annotest/AssemblyWS
    In [92]:
    mkdir MaSuRCA
  • Change directory to working directory, create symbolic links of FASTQ files.
    • In [93]:
    cd MaSuRCA

    /home/annotest/AssemblyWS/MaSuRCA
    In [94]:
    %%bash
ln -s ../FASTQ/* .
    In [95]:
    ls -l

    total 0
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:28 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1 26 Aug  7 16:28 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
  • Generate template of the config file
    • In [96]:
    %%bash
/share/apps/MaSuRCA-3.2.8/bin/masurca -G config.txt
  • Edit the config file to specify our raw reads

    • nano config.txt

    Change the contents as follow :

  PE= pe 300 50  cabV2_read1.fq.gz  cabV2_read2.fq.gz
  #JUMP= sh 3600 200  /FULL_PATH/short_1.fastq  /FULL_PATH/short_2.fastq
    In [98]:
    cat config.txt

    # example configuration file 

# DATA is specified as type {PE,JUMP,OTHER,PACBIO} and 5 fields:
# 1)two_letter_prefix 2)mean 3)stdev 4)fastq(.gz)_fwd_reads
# 5)fastq(.gz)_rev_reads. The PE reads are always assumed to be
# innies, i.e. --->.<---, and JUMP are assumed to be outties
# <---.--->. If there are any jump libraries that are innies, such as
# longjump, specify them as JUMP and specify NEGATIVE mean. Reverse reads
# are optional for PE libraries and mandatory for JUMP libraries. Any
# OTHER sequence data (454, Sanger, Ion torrent, etc) must be first
# converted into Celera Assembler compatible .frg files (see
# http://wgs-assembler.sourceforge.com)
DATA
#Illumina paired end reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#if single-end, do not specify <reverse_reads>
#MUST HAVE Illumina paired end reads to use MaSuRCA
PE= pe 300 50  cabV2_read1.fq.gz cabV2_read2.fq.gz
#Illumina mate pair reads supplied as <two-character prefix> <fragment mean> <fragment stdev> <forward_reads> <reverse_reads>
#JUMP= sh 3600 200  /FULL_PATH/short_1.fastq  /FULL_PATH/short_2.fastq
#pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
#if you have both types of reads supply them both as NANOPORE type
#PACBIO=/FULL_PATH/pacbio.fa
#NANOPORE=/FULL_PATH/nanopore.fa
#Other reads (Sanger, 454, etc) one frg file, concatenate your frg files into one if you have many
#OTHER=/FULL_PATH/file.frg
END

PARAMETERS
#set this to 1 if your Illumina jumping library reads are shorter than 100bp
EXTEND_JUMP_READS=0
#this is k-mer size for deBruijn graph values between 25 and 127 are supported, auto will compute the optimal size based on the read data and GC content
GRAPH_KMER_SIZE = auto
#set this to 1 for all Illumina-only assemblies
#set this to 0 if you have more than 15x coverage by long reads (Pacbio or Nanopore) or any other long reads/mate pairs (Illumina MP, Sanger, 454, etc)
USE_LINKING_MATES = 0
#specifies whether to run mega-reads correction on the grid
USE_GRID=0
#specifies queue to use when running on the grid MANDATORY
GRID_QUEUE=all.q
#batch size in the amount of long read sequence for each batch on the grid
GRID_BATCH_SIZE=300000000
#use at most this much coverage by the longest Pacbio or Nanopore reads
LHE_COVERAGE=30
#set to 1 to only do one pass of mega-reads, for faster but worse quality assembly
MEGA_READS_ONE_PASS=0
#this parameter is useful if you have too many Illumina jumping library mates. Typically set it to 60 for bacteria and 300 for the other organisms 
LIMIT_JUMP_COVERAGE = 300
#these are the additional parameters to Celera Assembler.  do not worry about performance, number or processors or batch sizes -- these are computed automatically. 
#set cgwErrorRate=0.25 for bacteria and 0.1<=cgwErrorRate<=0.15 for other organisms.
CA_PARAMETERS =  cgwErrorRate=0.15
#minimum count k-mers used in error correction 1 means all k-mers are used.  one can increase to 2 if Illumina coverage >100
KMER_COUNT_THRESHOLD = 1
#whether to attempt to close gaps in scaffolds with Illumina data
CLOSE_GAPS=1
#auto-detected number of cpus to use
NUM_THREADS = 16
#this is mandatory jellyfish hash size -- a safe value is estimated_genome_size*estimated_coverage
JF_SIZE = 200000000
#set this to 1 to use SOAPdenovo contigging/scaffolding module.  Assembly will be worse but will run faster. Useful for very large (>5Gbp) genomes from Illumina-only data
SOAP_ASSEMBLY=0
END
  • Generate the script file
    • In [99]:
    %%bash
/share/apps/MaSuRCA-3.2.8/bin/masurca config.txt

    Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run assembly
    In [100]:
    ls -l

    total 20
-rwxr-xr-x 1 jupyterhub1 jupyterhub1 13467 Aug  7 16:31 assemble.sh*
lrwxrwxrwx 1 jupyterhub1 jupyterhub1    26 Aug  7 16:28 cabV2_read1.fq.gz -> ../FASTQ/cabV2_read1.fq.gz
lrwxrwxrwx 1 jupyterhub1 jupyterhub1    26 Aug  7 16:28 cabV2_read2.fq.gz -> ../FASTQ/cabV2_read2.fq.gz
-rw-rw-r-- 1 jupyterhub1 jupyterhub1  3503 Aug  7 16:30 config.txt
  • Execute the assemble.sh script
    • In [101]:
    %%bash
./assemble.sh

    [Tue Aug  7 16:31:53 +07 2018] Processing pe library reads
[Tue Aug  7 16:31:55 +07 2018] Average PE read length 151
[Tue Aug  7 16:31:56 +07 2018] Using kmer size of 99 for the graph
[Tue Aug  7 16:31:56 +07 2018] MIN_Q_CHAR: 33
[Tue Aug  7 16:31:56 +07 2018] Creating mer database for Quorum
[Tue Aug  7 16:32:00 +07 2018] Error correct PE.
[Tue Aug  7 16:32:12 +07 2018] Estimating genome size.
[Tue Aug  7 16:32:16 +07 2018] Estimated genome size: 4694327
[Tue Aug  7 16:32:16 +07 2018] Creating k-unitigs with k=99
[Tue Aug  7 16:32:27 +07 2018] Computing super reads from PE 
[Tue Aug  7 16:32:31 +07 2018] Celera Assembler
[Tue Aug  7 16:32:32 +07 2018] ovlMerThreshold=75
[Tue Aug  7 16:33:08 +07 2018] Overlap/unitig success
[Tue Aug  7 16:33:08 +07 2018] recomputing A-stat for super-reads
[Tue Aug  7 16:33:34 +07 2018] recomputing A-stat for super-reads
[Tue Aug  7 16:33:36 +07 2018] Unitig consensus success
[Tue Aug  7 16:34:03 +07 2018] CA success
[Tue Aug  7 16:34:03 +07 2018] No gap closing possible.
[Tue Aug  7 16:34:08 +07 2018] Assembly complete, final scaffold sequences are in CA/final.genome.scf.fasta
[Tue Aug  7 16:34:08 +07 2018] All done

    =================================================================================================================

    QUAST : Quality Assessment Tool for Genome Assemblies

    Compare the quality of the assemblers

    Software is installed at /share/quast-5.0.0

    • Create directory for running QUAST
    In [102]:
    cd ..

    /home/annotest/AssemblyWS
    In [103]:
    mkdir QUAST
  • Change directory to working directory, create symbolic links of contigs files and reference file.
    • In [104]:
    cd QUAST

    /home/annotest/AssemblyWS/QUAST
    In [105]:
    %%bash
ln -s ../Velvet/Test_75/contigs.fa contigs_velvet_K75.fa
    In [106]:
    %%bash
ln -s ../VelvetOptimiser/auto_data_91/contigs.fa contigs_velvetOpt_K91.fa
    In [113]:
    %%bash
ln -s ../SPAdes/SPAdes_Out/contigs.fasta contigs_SPAdes.fa
    In [114]:
    %%bash
ln -s ../SPAdes/SPAdes_Out/scaffolds.fasta scaffolds_SPAdes.fa
    In [119]:
    %%bash
ln -s ../MaSuRCA/CA/final.genome.scf.fasta scaffolds_MaSuRCA.fa
    In [110]:
    %%bash
ln -s ../FASTA/cabV2.fa .
  • Run the QUAST
    • In [120]:
    %%bash
/share/apps/quast-5.0.0/quast.py -r cabV2.fa -t 4 contigs_velvet_K75.fa contigs_velvetOpt_K91.fa contigs_SPAdes.fa scaffolds_SPAdes.fa scaffolds_MaSuRCA.fa -o QUAST_Report

    /share/apps/quast-5.0.0/quast.py -r cabV2.fa -t 4 contigs_velvet_K75.fa contigs_velvetOpt_K91.fa contigs_SPAdes.fa scaffolds_SPAdes.fa scaffolds_MaSuRCA.fa -o QUAST_Report

Version: 5.0.0

System information:
  OS: Linux-3.10.0-514.26.2.el7.x86_64-x86_64-with-centos-7.4.1708-Core (linux_64)
  Python version: 3.5.5
  CPUs number: 144

Started: 2018-08-07 16:40:51

Logging to /home/annotest/AssemblyWS/QUAST/QUAST_Report/quast.log

CWD: /home/annotest/AssemblyWS/QUAST
Main parameters: 
  MODE: default, threads: 4, minimum contig length: 500, minimum alignment length: 65, \
  ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /home/annotest/AssemblyWS/QUAST/cabV2.fa ==> cabV2

Contigs:
  Pre-processing...
  1  contigs_velvet_K75.fa ==> contigs_velvet_K75
  2  contigs_velvetOpt_K91.fa ==> contigs_velvetOpt_K91
  3  contigs_SPAdes.fa ==> contigs_SPAdes
  4  scaffolds_SPAdes.fa ==> scaffolds_SPAdes
  5  scaffolds_MaSuRCA.fa ==> scaffolds_MaSuRCA

2018-08-07 16:40:56
Running Basic statistics processor...
  Reference genome:
    cabV2.fa, length = 4799920, num fragments = 1, GC % = 31.97
  Contig files: 
    1  contigs_velvet_K75
    2  contigs_velvetOpt_K91
    3  contigs_SPAdes
    4  scaffolds_SPAdes
    5  scaffolds_MaSuRCA
  Calculating N50 and L50...
    1  contigs_velvet_K75, N50 = 55329, L50 = 25, Total length = 4591890, GC % = 31.99, # N's per 100 kbp =  441.80
    2  contigs_velvetOpt_K91, N50 = 22892, L50 = 57, Total length = 4615405, GC % = 31.99, # N's per 100 kbp =  1012.61
    3  contigs_SPAdes, N50 = 8046, L50 = 171, Total length = 4589773, GC % = 31.98, # N's per 100 kbp =  0.00
    4  scaffolds_SPAdes, N50 = 49269, L50 = 29, Total length = 4644726, GC % = 31.99, # N's per 100 kbp =  1160.89
    5  scaffolds_MaSuRCA, N50 = 63511, L50 = 20, Total length = 4615776, GC % = 32.01, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/GC_content_plot.pdf
  Drawing contigs_velvet_K75 GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvet_K75_GC_content_plot.pdf
  Drawing contigs_velvetOpt_K91 GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvetOpt_K91_GC_content_plot.pdf
  Drawing contigs_SPAdes GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_SPAdes_GC_content_plot.pdf
  Drawing scaffolds_SPAdes GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/scaffolds_SPAdes_GC_content_plot.pdf
  Drawing scaffolds_MaSuRCA GC content plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/scaffolds_MaSuRCA_GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/coverage_histogram.pdf
  Drawing contigs_velvet_K75 coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvet_K75_coverage_histogram.pdf
  Drawing contigs_velvetOpt_K91 coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_velvetOpt_K91_coverage_histogram.pdf
  Drawing contigs_SPAdes coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/contigs_SPAdes_coverage_histogram.pdf
  Drawing scaffolds_SPAdes coverage histogram (bin size: 1x)...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/basic_stats/scaffolds_SPAdes_coverage_histogram.pdf
Done.

2018-08-07 16:41:01
Running Contig analyzer...
  1  contigs_velvet_K75
  1  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_contigs_velvet_K75.stdout and contigs_report_contigs_velvet_K75.stderr...
  1  Aligning contigs to the reference
  2  contigs_velvetOpt_K91
  2  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_contigs_velvetOpt_K91.stdout and contigs_report_contigs_velvetOpt_K91.stderr...
  2  Aligning contigs to the reference
  3  contigs_SPAdes
  3  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_contigs_SPAdes.stdout and contigs_report_contigs_SPAdes.stderr...
  3  Aligning contigs to the reference
  4  scaffolds_SPAdes
  4  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_scaffolds_SPAdes.stdout and contigs_report_scaffolds_SPAdes.stderr...
  4  Aligning contigs to the reference
  1  Analysis is finished.
  5  scaffolds_MaSuRCA
  5  Logging to files /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/contigs_report_scaffolds_MaSuRCA.stdout and contigs_report_scaffolds_MaSuRCA.stderr...
  5  Aligning contigs to the reference
  3  Analysis is finished.
  2  Analysis is finished.
  4  Analysis is finished.
  5  Analysis is finished.
  Creating total report...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/misassemblies_plot.pdf
  Drawing misassemblies FRCurve plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/contigs_reports/misassemblies_frcurve_plot.pdf
Done.

2018-08-07 16:41:08
Running NA-NGA calculation...
  1  contigs_velvet_K75, Largest alignment = 171055, NA50 = 44603, NGA50 = 43734, LA50 = 27, LGA50 = 29
  2  contigs_velvetOpt_K91, Largest alignment = 112338, NA50 = 20897, NGA50 = 19883, LA50 = 58, LGA50 = 63
  3  contigs_SPAdes, Largest alignment = 31311, NA50 = 8044, NGA50 = 7841, LA50 = 171, LGA50 = 185
  4  scaffolds_SPAdes, Largest alignment = 139088, NA50 = 44026, NGA50 = 42900, LA50 = 31, LGA50 = 33
  5  scaffolds_MaSuRCA, Largest alignment = 219320, NA50 = 63511, NGA50 = 62173, LA50 = 20, LGA50 = 22
  Drawing cumulative plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/aligned_stats/NGAx_plot.pdf
Done.

2018-08-07 16:41:09
Running Genome analyzer...
  NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.

  NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
  1  contigs_velvet_K75
  2  contigs_velvetOpt_K91
  3  contigs_SPAdes
  4  scaffolds_SPAdes
  1  Analysis is finished.
  5  scaffolds_MaSuRCA
  2  Analysis is finished.
  3  Analysis is finished.
  4  Analysis is finished.
  5  Analysis is finished.
  Drawing Genome fraction, % histogram...
    saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/genome_stats/genome_fraction_histogram.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2018-08-07 16:41:13
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2018-08-07 16:41:18
RESULTS:
  Text versions of total report are saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/report.html
  PDF version (tables and plots) is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/report.pdf
  Icarus (contig browser) is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/icarus.html
  Log is saved to /home/annotest/AssemblyWS/QUAST/QUAST_Report/quast.log

Finished: 2018-08-07 16:41:18
Elapsed time: 0:00:26.266695
NOTICEs: 3; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using QUAST!

    The report is generated in QUAST_Report directory.

  • Use ~/public_html to visualize the QUAST report
    • In [ ]:
    cd ~/public_html
    In [124]:
    cp -rp ../AssemblyWS/QUAST/QUAST_Report .
    In [125]:
    ls -l

    total 16
-rwxr-xr-x  1 annotest    annotest     151 Aug  1 02:48 index.html*
drwxrwxr-x 11 annotest    annotest    4096 Aug  1 03:10 JBrowse/
drwxrwxr-x  7 jupyterhub1 jupyterhub1 4096 Aug  7 16:41 QUAST_Report/
drwxrwxr-x  3 annotest    annotest    4096 Aug  6 21:33 Tomato/
  • Use your Web browser to visualize the QUAST report
    • In [ ]:
    http://breedserve.cab.kps.ku.ac.th/~annotest/QUAST_Report/report.html

    change ~annotest to your username

    In [126]:
    from IPython.display import HTML
HTML(filename="/home/annotest/public_html/QUAST_Report/report.html")
    Out[126]:

    QUAST

    Quality Assessment Tool for Genome Assemblies by CAB

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    {{ qualities }}
    {{ mainMetrics }}
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    {{ genesInContigs }}
    {{ operonsInContigs }}
    [{{ num_contigs }}, {{ Largest_alignment }}, {{ Total_aligned_length }}, {{ num_misassemblies }}, {{ Misassembled_contigs_length }}, {{ num_mismatches_per_100_kbp }}, {{ num_indels_per_100_kbp }}, {{ num_N's_per_100_kbp }}, {{ Genome_fraction }}, {{ Duplication_ratio }}, {{ NGA50 }}]
    {{ allMisassemblies }}
    {{ krona }}
    {"reference_index":5,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,1,3,1,1,6,7,16,26,54,54,113,152,246,309,437,599,684,841,1043,1082,1295,1330,1440,1467,1545,1616,1671,1750,1840,1856,1920,1929,2025,2016,1956,1912,1787,1653,1487,1351,1204,1011,866,697,554,419,335,285,202,162,95,97,65,54,44,26,25,24,20,6,11,5,7,3,3,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,3,1,3,6,14,13,29,51,53,97,152,219,339,496,593,737,868,973,1105,1262,1264,1393,1482,1543,1622,1696,1795,1821,1851,1877,2016,2041,2006,1941,1838,1817,1642,1511,1370,1196,993,829,670,579,433,352,266,206,164,105,94,59,73,35,38,21,21,16,7,7,7,3,3,3,2,2,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,1,0,0,2,2,5,8,16,35,42,61,115,157,236,327,487,568,755,815,1032,1139,1259,1241,1475,1486,1562,1586,1686,1753,1779,1940,1916,1993,2033,2044,1961,1833,1718,1708,1503,1377,1233,1030,826,688,572,446,328,272,196,156,141,79,68,41,37,36,25,17,20,14,10,7,3,3,2,1,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,1,0,0,2,2,6,4,20,24,53,59,117,176,228,334,440,648,723,901,984,1113,1251,1257,1402,1445,1577,1585,1718,1836,1769,1867,1973,1965,1997,2053,1970,1877,1742,1640,1475,1367,1238,1050,861,716,545,467,357,259,190,147,116,84,71,44,39,38,23,13,17,14,6,7,4,5,0,1,2,1,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,1,2,0,7,11,14,29,43,60,113,180,213,333,462,596,721,878,982,1153,1248,1304,1395,1491,1541,1693,1660,1797,1856,1859,1959,1987,2010,2010,2053,1849,1776,1720,1447,1357,1194,1045,837,735,620,427,318,272,198,162,141,105,80,56,36,28,30,18,15,8,8,4,4,4,2,1,1,1,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,2,2,1,0,3,7,15,13,35,47,76,107,160,230,334,493,575,710,886,1023,1088,1264,1324,1410,1563,1517,1624,1670,1779,1859,1865,1935,2002,2003,1988,1979,1880,1835,1678,1560,1382,1217,1012,856,688,559,387,361,256,229,143,129,93,84,47,39,27,26,15,13,14,8,6,1,5,4,2,0,1,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"filenames":["contigs_velvet_K75","contigs_velvetOpt_K91","contigs_SPAdes","scaffolds_SPAdes","scaffolds_MaSuRCA"],"lists_of_gc_info":null,"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,6,70,98,19,10,1,0,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,15,100,161,60,7,2,0,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,1,63,224,288,229,23,3,0,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,10,77,123,53,15,3,0,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,1,47,83,16,9,1,0,0,0,0,0,0,0,0,0,0,0]]]}
    {"links":["icarus_viewers/alignment_viewer.html"],"links_names":["View in Icarus contig browser"]}
    { "# contigs" : "is the total number of contigs in the assembly.", "Largest contig" : "is the length of the longest contig in the assembly.", "Total length" : "is the total number of bases in the assembly.", "Reference length" : "is the total number of bases in the reference.", "# contigs (>= 0 bp)" : "is the total number of contigs in the assembly that have size greater than or equal to 0 bp.", "Total length (>= 0 bp)" : "is the total number of bases in the contigs having size greater than or equal to 0 bp.", "N50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly. Usually there is no value that produces exactly 50%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 50% of the total assembly length.", "NG50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "N75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly. Usually there is no value that produces exactly 75%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 75% of the total assembly length.", "NG75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "L50" : "is the minimum number of contigs that produce half (50%) of the bases of the assembly. In other words, it's the number of contigs of length at least N50.", "LG50" : "is the minimum number of contigs that produce half (50%) of the bases of the reference genome. In other words, it's the number of contigs of length at least NG50. This metric is computed only if a reference genome is provided.", "L75" : "is the minimum number of contigs that produce 75% of the bases of the assembly. In other words, it's the number of contigs of length at least N75.", "LG75" : "is the minimum number of contigs that produce 75% of the bases of the reference genome. In other words, it's the number of contigs of length at least NG75. This metric is computed only if a reference genome is provided.", "NA50" : "is N50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NGA50" : "is NG50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NA75" : "is N75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NGA75" : "is NG75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "LA50" : "is L50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LGA50" : "is LG50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LA75" : "is L75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LGA75" : "is LG75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "Average %IDY" : "is the average of alignment identity percent (Nucmer measure of alignment accuracy) among all contigs.", "# misassemblies" : "is the number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).", "# large block misassemblies" : "is the number of misassemblies between alignments with length greater than or equal to 3 kbp and with the misassembly threshold equal to 5 kbp (instead of default 1 kbp for regular misassemblies).", "# misassembled contigs" : "is the number of contigs that contain misassembly events.", "Misassembled contigs length" : "is the number of total bases contained in all contigs that have one or more misassemblies.", "# relocations" : "is the number of relocation events among all misassembly events. Relocation is a misassembly where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference, or they overlap by more than 1 kbp and both flanking sequences align on the same chromosome.", "# translocations" : "is the number of translocation events among all misassembly events. Translocation is a misassembly where the flanking sequences align on different chromosomes.", "# interspecies translocations" : "is the number of interspecies translocation events among all misassembly events. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).", "# inversions" : "is the number of inversion events among all misassembly events. Inversion is a misassembly where it is not a relocation and the flanking sequences align on opposite strands of the same chromosome.", "# large relocations" : "is the number of relocation events among all large block misassemblies. Relocation is a misassembly where the left flanking sequence aligns over 5 kbp away from the right flanking sequence on the reference, or they overlap by more than 5 kbp and both flanking sequences align on the same chromosome.", "# large translocations" : "is the number of translocation events among all large block misassemblies. Translocation is a misassembly where the flanking sequences align on different chromosomes.", "# large i/s translocations" : "is the number of interspecies translocation events among all large block misassemblies. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).", "# large inversions" : "is the number of inversion events among all large block misassemblies. Inversion is a misassembly where it is not a relocation and the flanking sequences align on opposite strands of the same chromosome.", "# local misassemblies" : "is the number of local misassemblies. We define a local misassembly breakpoint as a breakpoint that satisfies these conditions:
    1. Two or more distinct alignments cover the breakpoint.
    2. The gap between left and right flanking sequences is less than the misassembly threshold (1 kbp by default).
    3. The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.
    ", "# scaffold gap ext. mis." : "is the number of scaffold gap size extensive misassemblies. We define a scaffold gap size misassembly as a breakpoint where the flanking sequences are combined in a scaffold on the wrong distance. These misassemblies are not included in the total number of misassemblies. ", "# scaffold gap loc. mis." : "is the number of scaffold gap size local misassemblies. Such breakpoints satisfy the local misassembly conditions but they occur inside scaffolds. These misassemblies are not included in the total number of local misassemblies. ", "# possibly misassembled contigs": "is the number of contigs that contain large unaligned fragment (default min length is 500 bp) and thus could possibly contain interspecies translocation with unknown reference.", "# possible misassemblies" : "is the number of putative interspecies translocations in possibly misassembled contigs if each large unaligned fragment is supposed to be a fragment of unknown reference.", "# intergenomic misassemblies" : "is the number of all found and putative (possible) interspecies translocations.", "# structural variations" : "is the number of misassemblies matched with structural variations.", "# possible TEs" : "is the number of misassemblies possibly caused by transposable elements (TEs). We define a possible TE as an event that satisfies these conditions:
    1. There are two misassembly breakpoints of the same type around a short alignment (less than 7 kbp by default)
    2. The gap between two long flanking sequences on the sides of the short alignment is less than 7 kbp.
    3. The long flanking sequences both are on the same strand of the same chromosome of the reference genome.
    ", "# unaligned mis. contigs" : "is the number of contigs that have the number of unaligned bases more than 50% of contig length and a misassembly event in their aligned fragment. Note that such misassemblies are not counted in # misassemblies and other misassemblies statistics.", "# fully unaligned contigs" : "is the number of contigs that have no alignment to the reference sequence.", "Fully unaligned length" : "is the total number of bases contained in all fully unaligned contigs. Uncalled bases (N's) are not counted.", "# partially unaligned contigs" : "is the number of contigs that have at least one alignment to the reference sequence but also have at least one unaligned fragment of length ≥ unaligned-part-size threshold.", "Partially unaligned length" : "is the total number of unaligned bases in all partially unaligned contigs. Uncalled bases (N's) are not counted.", "# ambiguous contigs" : "is the number of contigs that have reference alignments of equal quality in multiple locations on the reference.", "Ambiguous contigs length" : "is the total number of bases contained in all ambiguous contigs.", "Genome fraction (%)" : "is the total number of aligned bases in the reference, divided by the genome size. A base in the reference genome is counted as aligned if there is at least one contig with at least one alignment to this base. Contigs from repeat regions may map to multiple places, and thus may be counted multiple times in this quantity.", "GC (%)" : "is the total number of G and C nucleotides in the assembly, divided by the total length of the assembly.", "Reference GC (%)" : "is the total number of G and C nucleotides in the reference, divided by the total length of the reference.", "# mismatches per 100 kbp" : "is the average number of mismatches per 100000 aligned bases.", "# mismatches" : "is the number of mismatches in all aligned bases.", "# indels per 100 kbp" : "is the average number of indels per 100000 aligned bases.", "# indels" : "is the number of indels in all aligned bases", "# indels (<= 5 bp)" : "is the number of indels of length less than or equal to 5 bp", "# indels (> 5 bp)" : "is the number of indels of length greater than 5 bp", "Indels length" : "is the number of total bases contained in all indels", "# genomic features" : "is the number of genomic features (genes, transcripts, CDS) in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A feature counts as 'partially covered' if the assembly contains at least 100 bp of this feature but not the whole feature.", "# operons" : "is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as 'partially covered' if the assembly contains at least 100 bp of this operon but not the whole operon.", "# predicted genes (unique)" : "is the number of unique genes in the assembly found by a gene prediction tool.", "# predicted genes (>= 0 bp)" : "is the number of found genes having length greater than or equal to 0 bp.", "Cumulative length" : "plot shows the growth of assembly contig lengths. On the x-axis, contigs are ordered from largest (contig #1) to smallest. The y-axis gives the size of the x largest contigs in the assembly.", "Nx" : "plot shows the Nx metric value as x varies from 0 to 100. Nx is the minimum contig length y such that using contigs of length at least y accounts for at least x% of the total assembly length.", "NGx" : "plot shows the NGx metric value as x varies from 0 to 100. NGx is the minimum contig length y such that using contigs of length at least y accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "NAx" : "plot shows the NAx metric value as x varies from 0 to 100. NAx is computed similarly to Nx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken into aligned blocks at misassembly breakpoints. NAx is the minimum block length y such that using blocks of length at least y accounts for at least x% of the bases of the assembly. This metric is computed only if a reference genome is provided.", "NGAx" : "plot shows the NGAx metric value as x varies from 0 to 100.NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length y such that using blocks of length at least y accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "GC content" : "plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.", "Duplication ratio" : "is the total number of aligned bases in the assembly (i.e. Total length - Fully unaligned length - Partially unaligned length), divided by the total number of aligned bases in the reference (see the Genome fraction (%) metric). If the assembly contains many contigs that cover the same regions of the reference, its Duplication ratio may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.", "Largest alignment" : "is the length of the largest continuous alignment in the assembly. This metric is always equal to the Largest contig metric but it can be smaller if the largest contig of the assembly contains a misassembly event.", "Total aligned length" : "is the total number of aligned bases in the assembly.", "Avg contig read support" : "is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).", "# N's" : "is the total number of uncalled bases (N's) in the assembly.", "# N's per 100 kbp" : "is the average number of uncalled bases (N's) per 100000 assembly bases.", "# mapped" : "is the number of reads that mapped to the assembly.", "Mapped (%)" : "is the percent of reads that mapped to the assembly.", "# properly paired" : "is the number of reads that mapped within expected range and orientation of each other to the assembly.", "Properly paired (%)" : "is the percent of reads that mapped within expected range and orientation of each other to the assembly.", "# singletons" : "is the number of reads which do not overlap any other reads.", "Singletons (%)" : "is the percent of reads which do not overlap any other reads.", "# misjoint mates" : "is the number of reads with mate mapped to a different contig.", "Misjoint mates (%)" : "is the percent of reads with mate mapped to a different contig.", "Avg. coverage depth" : "is the average depth of coverage.", "Coverage >= 1x (%)" : "is the total number of bases with at least 1x coverage, divided by the total length of the assembly.", "# similar correct contigs" : "is the number of correct contigs similar among > 50% assemblies (see Icarus for visualization).", "# similar misassembled blocks" : "is the number of misassembled blocks similar among > 50% assemblies (see Icarus for visualization)." }