Update bacterial assembly WF - change shovill assembler

[hugolefeuvre]

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
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• In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
• Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

• ❌ bacterial_genome_assembly.ga_0

  Problems:

  • Output with path /tmp/tmpl_poj8ez/shovill_contigs_graph__556a2824-4c8d-43d6-a546-a0ab39ac4894.txt different than expected
    Expected text 'KC:i' in output ('')
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Input adapter trimmed sequence reads (forward):

      • step_state: scheduled

    • Step 2: Input adapter trimmed sequence reads (reverse):

      • step_state: scheduled

    • Step 3: Shovill genome assembly (toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/shovill:1.1.0--hdfd78af_2

          Command Line:

          • cp '/tmp/tmp_5geeevs/files/d/8/8/dataset_d88c0cb7-6dd1-4e19-8813-8d6523b89d83.dat' fastq_r1.'fastqsanger.gz' && cp '/tmp/tmp_5geeevs/files/0/3/4/dataset_0343ffce-0126-4755-a9ee-10bfc3619d30.dat' fastq_r2.'fastqsanger.gz' &&  GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-4096}/1024)) && SHOVILL_RAM=${SHOVILL_RAM:-${GALAXY_MEMORY_GB}} &&  shovill --outdir 'out' --cpus ${GALAXY_SLOTS:-1} --ram ${SHOVILL_RAM:-4} --R1 'fastq_r1.fastqsanger.gz' --R2 'fastq_r2.fastqsanger.gz'  --namefmt 'contig%05d' --depth '100' --minlen 0 --mincov 2 --assembler skesa --keepfiles

          Exit Code:

          • 0

          Standard Error:

          • [shovill] Hello stranger
            [shovill] You ran: /usr/local/bin/shovill --outdir out --cpus 1 --ram 4 --R1 fastq_r1.fastqsanger.gz --R2 fastq_r2.fastqsanger.gz --namefmt contig%05d --depth 100 --minlen 0 --mincov 2 --assembler skesa --keepfiles
            [shovill] This is shovill 1.1.0
            [shovill] Written by Torsten Seemann
            [shovill] Homepage is https://github.com/tseemann/shovill
            [shovill] Operating system is linux
            [shovill] Perl version is v5.32.1
            [shovill] Machine has 4 CPU cores and 15.61 GB RAM
            [shovill] Using bwa - /usr/local/bin/bwa | Version: 0.7.19-r1273
            [shovill] Using flash - /usr/local/bin/flash | FLASH v1.2.11
            [shovill] Using java - /usr/local/bin/java | openjdk version "24.0.2-internal" 2025-07-15
            [shovill] Using kmc - /usr/local/bin/kmc | K-Mer Counter (KMC) ver. 3.2.4 (2024-02-09)
            [shovill] Using lighter - /usr/local/bin/lighter | Lighter v1.1.3
            [shovill] Using megahit - /usr/local/bin/megahit | MEGAHIT v1.2.9
            [shovill] Using megahit_toolkit - /usr/local/bin/megahit_toolkit | v1.2.9
            [shovill] Using pigz - /usr/local/bin/pigz | pigz 2.8
            [shovill] Using pilon - /usr/local/bin/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
            [shovill] Using samclip - /usr/local/bin/samclip | samclip 0.4.0
            [shovill] Using samtools - /usr/local/bin/samtools | Version: 1.22.1 (using htslib 1.22.1)
            [shovill] Using seqtk - /usr/local/bin/seqtk | Version: 1.5-r133
            [shovill] Using skesa - /usr/local/bin/skesa | SKESA 2.5.1
            [shovill] Using spades.py - /usr/local/bin/spades.py | SPAdes genome assembler v4.2.0
            [shovill] Using trimmomatic - /usr/local/bin/trimmomatic | 0.40
            [shovill] Using velvetg - /usr/local/bin/velvetg | Version 1.2.10
            [shovill] Using velveth - /usr/local/bin/velveth | Version 1.2.10
            [shovill] Found spades version: 004002000
            [shovill] Using tempdir: /tmp/tmp_5geeevs/job_working_directory/000/3/tmp
            [shovill] Changing into folder: /tmp/tmp_5geeevs/job_working_directory/000/3/working/out
            [shovill] Collecting raw read statistics with 'seqtk'
            [shovill] Running: seqtk fqchk -q3 \/tmp\/tmp_5geeevs\/job_working_directory\/000\/3\/working\/fastq_r1\.fastqsanger\.gz >/tmp/tmp_5geeevs/job_working_directory/000/3/tmp/_phH9ZovSU 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log
            [shovill] Read stats: max_len = 301
            [shovill] Read stats: min_len = 35
            [shovill] Read stats: avg_len = 201
            [shovill] Read stats: total_bp = 59339800
            [shovill] Estimating genome size by counting unqiue 21-mers > frequency 10 
            [shovill] Running: kmc -sm -m2 -t1 -k21 -ci10 \/tmp\/tmp_5geeevs\/job_working_directory\/000\/3\/working\/fastq_r1\.fastqsanger\.gz /tmp/tmp_5geeevs/job_working_directory/000/3/tmp/DnZ_xn_QRa/kmc /tmp/tmp_5geeevs/job_working_directory/000/3/tmp/DnZ_xn_QRa 2>&1 | sed 's/^/[kmc] /' | tee -a shovill.log
            [shovill] Using genome size 932868 bp
            [shovill] Estimated sequencing depth: 63 x
            [shovill] No read depth reduction requested or necessary.
            [shovill] Appending -Xmx4g to _JAVA_OPTIONS
            [shovill] Running: ln -sf \/tmp\/tmp_5geeevs\/job_working_directory\/000\/3\/working\/fastq_r1\.fastqsanger\.gz R1.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log
            [shovill] Running: ln -sf \/tmp\/tmp_5geeevs\/job_working_directory\/000\/3\/working\/fastq_r2\.fastqsanger\.gz R2.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log
            [shovill] Average read length looks like 201 bp
            [shovill] Automatically setting --minlen to 100
            [shovill] Setting k-mer range to (31 .. 127)
            [shovill] Estimated K-mers: 31 55 79 103 127 [kn=5, ks=24, kmin=31, kmax=127]
            [shovill] Using kmers: 31,55,79,103,127
            [shovill] Correcting reads with 'Lighter'
            [shovill] Running: lighter -od . -r R1.fq.gz -r R2.fq.gz -K 32 932868 -t 1 -maxcor 1 2>&1 | sed 's/^/[lighter] /' | tee -a shovill.log
            [shovill] Overlapping/stitching PE reads with 'FLASH'
            [shovill] Running: flash -m 20 -M 301 -d . -o flash -z -t 1 R1.cor.fq.gz R2.cor.fq.gz 2>&1 | sed 's/^//' | tee -a shovill.log
            [shovill] Assembling reads with 'skesa'
            [shovill] Running: skesa --gz  --fastq flash.extendedFrags.fastq.gz --fastq flash.notCombined_1.fastq.gz,flash.notCombined_2.fastq.gz --use_paired_ends --contigs_out skesa.fasta --min_contig 1 --memory 4 --cores 1 --vector_percent 1 2>&1 | sed 's/^/[skesa] /' | tee -a shovill.log
            [shovill] Checking for assembly errors in skesa.fasta
            [shovill] Running: bwa index skesa.fasta 2>&1 | sed 's/^/[bwa-index] /' | tee -a shovill.log
            [shovill] Running: samtools faidx skesa.fasta 2>&1 | sed 's/^/[faidx] /' | tee -a shovill.log
            [shovill] Running: (bwa mem -v 3 -x intractg -t 1 skesa.fasta R1.fq.gz R2.fq.gz | samclip --ref skesa.fasta.fai | samtools sort --threads 1 -m 2048m --reference skesa.fasta -T /tmp/tmp_5geeevs/job_working_directory/000/3/tmp -o shovill.bam) 2>&1 | sed 's/^/[bwa+samtools-sort] /' | tee -a shovill.log
            [shovill] Running: samtools index shovill.bam 2>&1 | sed 's/^/[samtools-index] /' | tee -a shovill.log
            [shovill] Correcting errors in skesa.fasta
            [shovill] Running: pilon --genome skesa.fasta --frags shovill.bam --minmq 60 --minqual 3 --fix bases --output pilon --threads 1 --changes --mindepth 0.25 2>&1 | sed 's/^/[pilon] /' | tee -a shovill.log
            [shovill] Repaired 391 contigs from skesa.fasta at 649 positions.
            [shovill] Assembly is 2836204, estimated genome size was 932868 (+204.03%)
            [shovill] Note: skesa does not produce a graph file
            [shovill] Walltime used: 1 min 52 sec
            [shovill] Results in: /tmp/tmp_5geeevs/job_working_directory/000/3/working/out
            [shovill] Final assembly contigs: /tmp/tmp_5geeevs/job_working_directory/000/3/working/out/contigs.fa
            [shovill] It contains 909 (min=100) contigs totalling 2836204 bp.
            [shovill] The name 'shovill' is pronounced as 'shovel' in English
            [shovill] Done.
            

          Standard Output:

          • [kmc] ***********************
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            [kmc] 
            [kmc] 
            [kmc] 1st stage: 1.118s
            [kmc] 2nd stage: 2.47619s
            [kmc] 3rd stage: 0.003157s
            [kmc] Total    : 3.59734s
            [kmc] Tmp size : 33MB
            [kmc] Tmp size strict memory : 0MB
            [kmc] Tmp total: 33MB
            [kmc] 
            [kmc] Stats:
            [kmc]    No. of k-mers below min. threshold :      3020760
            [kmc]    No. of k-mers above max. threshold :            0
            [kmc]    No. of unique k-mers               :      3953628
            [kmc]    No. of unique counted k-mers       :       932868
            [kmc]    Total no. of k-mers                :     26713100
            [kmc]    Total no. of reads                 :       147840
            [kmc]    Total no. of super-k-mers          :      4068972
            [lighter] [2026-04-15 09:23:58] =============Start====================
            [lighter] [2026-04-15 09:23:58] Scanning the input files to infer alpha(sampling rate)
            [lighter] [2026-04-15 09:23:58] Average coverage is 63.493 and alpha is 0.110
            [lighter] [2026-04-15 09:23:59] Bad quality threshold is ")"
            [lighter] [2026-04-15 09:24:00] Finish sampling kmers
            [lighter] [2026-04-15 09:24:00] Bloom filter A's false positive rate: 0.161268
            [lighter] [2026-04-15 09:24:06] Finish storing trusted kmers
            [lighter] [2026-04-15 09:24:13] Finish error correction
            [lighter] Processed 295680 reads:
            [lighter] 	217994 are error-free
            [lighter] 	Corrected 87725 bases(1.129225 corrections for reads with errors)
            [lighter] 	Trimmed 0 reads with average trimmed bases 0.000000
            [lighter] 	Discard 0 reads
            [FLASH] Starting FLASH v1.2.11
            [FLASH] Fast Length Adjustment of SHort reads
            [FLASH]  
            [FLASH] Input files:
            [FLASH]     R1.cor.fq.gz
            [FLASH]     R2.cor.fq.gz
            [FLASH]  
            [FLASH] Output files:
            [FLASH]     ./flash.extendedFrags.fastq.gz
            [FLASH]     ./flash.notCombined_1.fastq.gz
            [FLASH]     ./flash.notCombined_2.fastq.gz
            [FLASH]     ./flash.hist
            [FLASH]     ./flash.histogram
            [FLASH]  
            [FLASH] Parameters:
            [FLASH]     Min overlap:           20
            [FLASH]     Max overlap:           301
            [FLASH]     Max mismatch density:  0.250000
            [FLASH]     Allow "outie" pairs:   false
            [FLASH]     Cap mismatch quals:    false
            [FLASH]     Combiner threads:      1
            [FLASH]     Input format:          FASTQ, phred_offset=33
            [FLASH]     Output format:         FASTQ, phred_offset=33, gzip
            [FLASH]  
            [FLASH] Starting reader and writer threads
            [FLASH] Starting 1 combiner threads
            [FLASH] Processed 25000 read pairs
            [FLASH] Processed 50000 read pairs
            [FLASH] Processed 75000 read pairs
            [FLASH] Processed 100000 read pairs
            [FLASH] Processed 125000 read pairs
            [FLASH] Processed 147840 read pairs
            [FLASH]  
            [FLASH] Read combination statistics:
            [FLASH]     Total pairs:      147840
            [FLASH]     Combined pairs:   143166
            [FLASH]     Uncombined pairs: 4674
            [FLASH]     Percent combined: 96.84%
            [FLASH]  
            [FLASH] Writing histogram files.
            [FLASH]  
            [FLASH] FLASH v1.2.11 complete!
            [FLASH] 13.926 seconds elapsed
            [skesa] skesa --gz --fastq flash.extendedFrags.fastq.gz --fastq flash.notCombined_1.fastq.gz,flash.notCombined_2.fastq.gz --use_paired_ends --contigs_out skesa.fasta --min_contig 1 --memory 4 --cores 1 --vector_percent 1 
            [skesa] 
            [skesa] WARNING: option --gz is deprecated - gzipped files are now recognized automatically
            [skesa] Total mates: 152514 Paired reads: 4674
            [skesa] Reads acquired in  1.788907s wall, 1.750000s user + 0.020000s system = 1.770000s CPU (98.9%)
            [skesa] Adapters clip is disabled
            [skesa] 
            [skesa] Kmer len: 21
            [skesa] Raw kmers: 30617284 Memory needed (GB): 0.587852 Memory available (GB): 1.9863 1 cycle(s) will be performed
            [skesa] Distinct kmers: 3001161
            [skesa] Kmer count in  4.756322s wall, 4.700000s user + 0.060000s system = 4.760000s CPU (100.1%)
            [skesa] Uniq kmers merging in  0.071685s wall, 0.050000s user + 0.010000s system = 0.060000s CPU (83.7%)
            [skesa] Kmers branching in  4.033555s wall, 4.020000s user + 0.020000s system = 4.040000s CPU (100.2%)
            [skesa] 
            [skesa] Average read length: 221
            [skesa] Genome size estimate: 2784375
            [skesa] 
            [skesa] Kmer: 21 Graph size: 3001161 Contigs in: 0
            [skesa] Valley: 2
            [skesa] 
            [skesa] Mark used kmers in  0.000004s wall, 0.000000s user + 0.000000s system = 0.000000s CPU (n/a%)
            [skesa] Kmers in multiple/single contigs: 0 0
            [skesa] Fragments before: 1533 2964594
            [skesa] Fragments after: 1533 2964594
            [skesa] New seeds: 1341
            [skesa] New seeds in  2.800160s wall, 2.790000s user + 0.010000s system = 2.800000s CPU (100.0%)
            [skesa] Fragments before: 2682 56322
            [skesa] Fragments after: 2682 56322
            [skesa] Connectors: 0 Extenders: 2682
            [skesa] Connections and extensions in  0.750919s wall, 0.750000s user + 0.010000s system = 0.760000s CPU (101.2%)
            [skesa] Contigs out: 1341 Genome: 2914638 N50: 4131 L50: 222
            [skesa] Assembled in  3.567063s wall, 3.550000s user + 0.020000s system = 3.570000s CPU (100.1%)
            [skesa] 
            [skesa] 
            [skesa] Average count: 8.93619 Max kmer: 21
            [skesa] Connected: 3680 ambiguously connected: 276 from 4674 mate pairs
            [skesa] Connect pairs in  14.369715s wall, 14.320000s user + 0.050000s system = 14.370000s CPU (100.0%)
            [skesa] 
            [skesa] N50 for inserts: 645
            [skesa] 
            [skesa] Seed kmers: 0
            [skesa] Cleaned reads: 28003
            [skesa] Reads for connection: 2146
            [skesa] Internal reads: 160
            [skesa] Reads cleaned in  2.737589s wall, 2.720000s user + 0.010000s system = 2.730000s CPU (99.7%)
            [skesa] WARNING: iterations are disabled
            [skesa] 
            [skesa] Connecting mate pairs using kmer length: 21
            [skesa] Connected: 631 ambiguously connected: 199 from 1073 mate pairs
            [skesa] Connect pairs in  3.580334s wall, 3.560000s user + 0.020000s system = 3.580000s CPU (100.0%)
            [skesa] Totally connected: 631
            [skesa] Added notconnected: 398
            [skesa] 
            [skesa] Kmer len: 25
            [skesa] Raw kmers: 545004 Memory needed (GB): 0.0104641 Memory available (GB): 1.9367 1 cycle(s) will be performed
            [skesa] Distinct kmers: 94886
            [skesa] Kmer count in  0.070613s wall, 0.070000s user + 0.000000s system = 0.070000s CPU (99.1%)
            [skesa] Uniq kmers merging in  0.002017s wall, 0.000000s user + 0.000000s system = 0.000000s CPU (n/a%)
            [skesa] Kmers branching in  0.091327s wall, 0.090000s user + 0.000000s system = 0.090000s CPU (98.5%)
            [skesa] Kmer: 25 Graph size: 94886 Contigs in: 1341
            [skesa] Valley: 0
            [skesa] 
            [skesa] Mark used kmers in  0.521850s wall, 0.520000s user + 0.000000s system = 0.520000s CPU (99.6%)
            [skesa] Kmers in multiple/single contigs: 0 81642
            [skesa] Fragments before: 221 11683
            [skesa] Fragments after: 221 11683
            [skesa] New seeds: 20
            [skesa] New seeds in  0.019790s wall, 0.020000s user + 0.000000s system = 0.020000s CPU (101.1%)
            [skesa] Fragments before: 324 8376
            [skesa] Fragments after: 230 8376
            [skesa] Connectors: 94 Extenders: 136
            [skesa] Connections and extensions in  0.555541s wall, 0.550000s user + 0.010000s system = 0.560000s CPU (100.8%)
            [skesa] Contigs out: 1267 Genome: 2920257 N50: 4527 L50: 202
            [skesa] Assembled in  1.097799s wall, 1.090000s user + 0.010000s system = 1.100000s CPU (100.2%)
            [skesa] 
            [skesa] 
            [skesa] Kmer len: 269
            [skesa] Raw kmers: 281872 Memory needed (GB): 0.0270597 Memory available (GB): 1.93204 1 cycle(s) will be performed
            [skesa] Distinct kmers: 37018
            [skesa] Kmer count in  0.080413s wall, 0.080000s user + 0.000000s system = 0.080000s CPU (99.5%)
            [skesa] Uniq kmers merging in  0.001425s wall, 0.000000s user + 0.000000s system = 0.000000s CPU (n/a%)
            [skesa] Kmers branching in  0.073174s wall, 0.080000s user + 0.000000s system = 0.080000s CPU (109.3%)
            [skesa] Kmer: 269 Graph size: 37018 Contigs in: 1267
            [skesa] Valley: 0
            [skesa] 
            [skesa] Mark used kmers in  0.764632s wall, 0.760000s user + 0.000000s system = 0.760000s CPU (99.4%)
            [skesa] Kmers in multiple/single contigs: 0 34185
            [skesa] Fragments before: 26 1408
            [skesa] Fragments after: 26 1408
            [skesa] New seeds: 0
            [skesa] New seeds in  0.005021s wall, 0.010000s user + 0.000000s system = 0.010000s CPU (199.2%)
            [skesa] Fragments before: 27 1408
            [skesa] Fragments after: 26 1408
            [skesa] Connectors: 1 Extenders: 25
            [skesa] Connections and extensions in  0.568702s wall, 0.560000s user + 0.000000s system = 0.560000s CPU (98.5%)
            [skesa] Contigs out: 1045 Genome: 2887125 N50: 4570 L50: 198
            [skesa] Assembled in  1.338653s wall, 1.330000s user + 0.000000s system = 1.330000s CPU (99.4%)
            [skesa] 
            [skesa] 
            [skesa] Kmer len: 511
            [skesa] Raw kmers: 118354 Memory needed (GB): 0.0193154 Memory available (GB): 1.92606 1 cycle(s) will be performed
            [skesa] Distinct kmers: 10574
            [skesa] Kmer count in  0.037516s wall, 0.040000s user + 0.000000s system = 0.040000s CPU (106.6%)
            [skesa] Uniq kmers merging in  0.000623s wall, 0.000000s user + 0.000000s system = 0.000000s CPU (n/a%)
            [skesa] Kmers branching in  0.024339s wall, 0.020000s user + 0.000000s system = 0.020000s CPU (82.2%)
            [skesa] Kmer: 511 Graph size: 10574 Contigs in: 1045
            [skesa] Valley: 0
            [skesa] 
            [skesa] Mark used kmers in  0.701172s wall, 0.700000s user + 0.000000s system = 0.700000s CPU (99.8%)
            [skesa] Kmers in multiple/single contigs: 0 9740
            [skesa] Fragments before: 10 552
            [skesa] Fragments after: 10 552
            [skesa] New seeds: 0
            [skesa] New seeds in  0.002281s wall, 0.000000s user + 0.010000s system = 0.010000s CPU (438.4%)
            [skesa] Fragments before: 10 552
            [skesa] Fragments after: 10 552
            [skesa] Connectors: 0 Extenders: 10
            [skesa] Connections and extensions in  0.601409s wall, 0.600000s user + 0.000000s system = 0.600000s CPU (99.8%)
            [skesa] Contigs out: 909 Genome: 2836205 N50: 4605 L50: 192
            [skesa] Assembled in  1.305051s wall, 1.300000s user + 0.010000s system = 1.310000s CPU (100.4%)
            [skesa] 
            [skesa] DONE
            [bwa-index] [bwa_index] Pack FASTA... 0.01 sec
            [bwa-index] [bwa_index] Construct BWT for the packed sequence...
            [bwa-index] [bwa_index] 0.47 seconds elapse.
            [bwa-index] [bwa_index] Update BWT... 0.01 sec
            [bwa-index] [bwa_index] Pack forward-only FASTA... 0.01 sec
            [bwa-index] [bwa_index] Construct SA from BWT and Occ... 0.21 sec
            [bwa-index] [main] Version: 0.7.19-r1273
            [bwa-index] [main] CMD: bwa index skesa.fasta
            [bwa-index] [main] Real time: 0.715 sec; CPU: 0.711 sec
            [bwa+samtools-sort] [M::bwa_idx_load_from_disk] read 0 ALT contigs
            [bwa+samtools-sort] [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
            [bwa+samtools-sort] [samclip] Loading: skesa.fasta.fai
            [bwa+samtools-sort] [samclip] Found 909 sequences in skesa.fasta.fai
            [bwa+samtools-sort] [M::process] read 50010 sequences (10000190 bp)...
            [bwa+samtools-sort] [M::process] read 49994 sequences (10000229 bp)...
            [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 24022, 0, 0)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR...
            [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (132, 186, 274)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 558)
            [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (207.75, 106.26)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 700)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs
            [bwa+samtools-sort] [M::mem_process_seqs] Processed 50010 reads in 3.000 CPU sec, 3.002 real sec
            [bwa+samtools-sort] [M::process] read 49858 sequences (10000286 bp)...
            [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 23935, 0, 0)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR...
            [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (132, 187, 271)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 549)
            [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (206.51, 104.22)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 688)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs
            [bwa+samtools-sort] [M::mem_process_seqs] Processed 49994 reads in 3.117 CPU sec, 3.365 real sec
            [bwa+samtools-sort] [samclip] Processed 100000 records...
            [bwa+samtools-sort] [M::process] read 49916 sequences (10000247 bp)...
            [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 23847, 0, 0)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR...
            [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (133, 187, 273)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 553)
            [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (207.71, 104.79)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 693)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs
            [bwa+samtools-sort] [M::mem_process_seqs] Processed 49858 reads in 3.109 CPU sec, 3.352 real sec
            [bwa+samtools-sort] [M::process] read 49730 sequences (10000334 bp)...
            [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 23882, 0, 0)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR...
            [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (133, 186, 273)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 553)
            [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (207.40, 103.92)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 693)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs
            [bwa+samtools-sort] [M::mem_process_seqs] Processed 49916 reads in 3.135 CPU sec, 3.399 real sec
            [bwa+samtools-sort] [samclip] Processed 200000 records...
            [bwa+samtools-sort] [M::process] read 46172 sequences (9229662 bp)...
            [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 23807, 0, 0)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR...
            [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (134, 188, 276)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 560)
            [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (209.40, 106.58)
            [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 702)
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs
            [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs
            [bwa+samtools-sort] [M::mem_process_seqs] Processed 49730 reads in 3.098 CPU sec, 3.357 real sec
            [bwa+samtools-sort] [M::mem_p
            ..
            ting Contig_785_8.87459:1-2771 changes to pilon.changes
            [pilon] Writing updated Contig_785_8.87459_pilon to pilon.fasta
            [pilon] Writing Contig_786_8.13443:1-2988 changes to pilon.changes
            [pilon] Writing updated Contig_786_8.13443_pilon to pilon.fasta
            [pilon] Writing Contig_787_6.8737:1-1556 changes to pilon.changes
            [pilon] Writing updated Contig_787_6.8737_pilon to pilon.fasta
            [pilon] Writing Contig_788_7.60679:1-1228 changes to pilon.changes
            [pilon] Writing updated Contig_788_7.60679_pilon to pilon.fasta
            [pilon] Writing Contig_789_7.9644:1-947 changes to pilon.changes
            [pilon] Writing updated Contig_789_7.9644_pilon to pilon.fasta
            [pilon] Writing Contig_790_9.61068:1-17106 changes to pilon.changes
            [pilon] Writing updated Contig_790_9.61068_pilon to pilon.fasta
            [pilon] Writing Contig_791_16.3827:1-2487 changes to pilon.changes
            [pilon] Writing updated Contig_791_16.3827_pilon to pilon.fasta
            [pilon] Writing Contig_792_9.81192:1-6363 changes to pilon.changes
            [pilon] Writing updated Contig_792_9.81192_pilon to pilon.fasta
            [pilon] Writing Contig_793_8.20412:1-990 changes to pilon.changes
            [pilon] Writing updated Contig_793_8.20412_pilon to pilon.fasta
            [pilon] Writing Contig_794_9.66448:1-3832 changes to pilon.changes
            [pilon] Writing updated Contig_794_9.66448_pilon to pilon.fasta
            [pilon] Writing Contig_795_9.32098:1-3151 changes to pilon.changes
            [pilon] Writing updated Contig_795_9.32098_pilon to pilon.fasta
            [pilon] Writing Contig_796_9.18186:1-4430 changes to pilon.changes
            [pilon] Writing updated Contig_796_9.18186_pilon to pilon.fasta
            [pilon] Writing Contig_797_8.74157:1-1266 changes to pilon.changes
            [pilon] Writing updated Contig_797_8.74157_pilon to pilon.fasta
            [pilon] Writing Contig_798_11.1627:1-1157 changes to pilon.changes
            [pilon] Writing updated Contig_798_11.1627_pilon to pilon.fasta
            [pilon] Writing Contig_799_9.10599:1-1539 changes to pilon.changes
            [pilon] Writing updated Contig_799_9.10599_pilon to pilon.fasta
            [pilon] Writing Contig_800_9.53861:1-3180 changes to pilon.changes
            [pilon] Writing updated Contig_800_9.53861_pilon to pilon.fasta
            [pilon] Writing Contig_801_8.31373:1-1958 changes to pilon.changes
            [pilon] Writing updated Contig_801_8.31373_pilon to pilon.fasta
            [pilon] Writing Contig_802_8.66061:1-2498 changes to pilon.changes
            [pilon] Writing updated Contig_802_8.66061_pilon to pilon.fasta
            [pilon] Writing Contig_803_8.02256:1-1084 changes to pilon.changes
            [pilon] Writing updated Contig_803_8.02256_pilon to pilon.fasta
            [pilon] Writing Contig_804_12.4163:1-1543 changes to pilon.changes
            [pilon] Writing updated Contig_804_12.4163_pilon to pilon.fasta
            [pilon] Writing Contig_805_19.1814:1-18608 changes to pilon.changes
            [pilon] Writing updated Contig_805_19.1814_pilon to pilon.fasta
            [pilon] Writing Contig_806_11.1424:1-701 changes to pilon.changes
            [pilon] Writing updated Contig_806_11.1424_pilon to pilon.fasta
            [pilon] Writing Contig_807_7.23455:1-570 changes to pilon.changes
            [pilon] Writing updated Contig_807_7.23455_pilon to pilon.fasta
            [pilon] Writing Contig_808_6.99033:1-2191 changes to pilon.changes
            [pilon] Writing updated Contig_808_6.99033_pilon to pilon.fasta
            [pilon] Writing Contig_809_8.99615:1-1318 changes to pilon.changes
            [pilon] Writing updated Contig_809_8.99615_pilon to pilon.fasta
            [pilon] Writing Contig_810_8.66969:1-3768 changes to pilon.changes
            [pilon] Writing updated Contig_810_8.66969_pilon to pilon.fasta
            [pilon] Writing Contig_811_7.77895:1-2861 changes to pilon.changes
            [pilon] Writing updated Contig_811_7.77895_pilon to pilon.fasta
            [pilon] Writing Contig_812_10.2169:1-1062 changes to pilon.changes
            [pilon] Writing updated Contig_812_10.2169_pilon to pilon.fasta
            [pilon] Writing Contig_813_9.16934:1-894 changes to pilon.changes
            [pilon] Writing updated Contig_813_9.16934_pilon to pilon.fasta
            [pilon] Writing Contig_814_9.51006:1-2853 changes to pilon.changes
            [pilon] Writing updated Contig_814_9.51006_pilon to pilon.fasta
            [pilon] Writing Contig_815_8.34526:1-663 changes to pilon.changes
            [pilon] Writing updated Contig_815_8.34526_pilon to pilon.fasta
            [pilon] Writing Contig_816_9.72982:1-912 changes to pilon.changes
            [pilon] Writing updated Contig_816_9.72982_pilon to pilon.fasta
            [pilon] Writing Contig_817_8.35911:1-1145 changes to pilon.changes
            [pilon] Writing updated Contig_817_8.35911_pilon to pilon.fasta
            [pilon] Writing Contig_818_43.8233:1-750 changes to pilon.changes
            [pilon] Writing updated Contig_818_43.8233_pilon to pilon.fasta
            [pilon] Writing Contig_819_8.84317:1-3272 changes to pilon.changes
            [pilon] Writing updated Contig_819_8.84317_pilon to pilon.fasta
            [pilon] Writing Contig_820_9.58771:1-2688 changes to pilon.changes
            [pilon] Writing updated Contig_820_9.58771_pilon to pilon.fasta
            [pilon] Writing Contig_821_9.79373:1-2764 changes to pilon.changes
            [pilon] Writing updated Contig_821_9.79373_pilon to pilon.fasta
            [pilon] Writing Contig_822_9.69278:1-4131 changes to pilon.changes
            [pilon] Writing updated Contig_822_9.69278_pilon to pilon.fasta
            [pilon] Writing Contig_823_9.29861:1-2036 changes to pilon.changes
            [pilon] Writing updated Contig_823_9.29861_pilon to pilon.fasta
            [pilon] Writing Contig_824_9.31214:1-539 changes to pilon.changes
            [pilon] Writing updated Contig_824_9.31214_pilon to pilon.fasta
            [pilon] Writing Contig_825_12.0659:1-566 changes to pilon.changes
            [pilon] Writing updated Contig_825_12.0659_pilon to pilon.fasta
            [pilon] Writing Contig_826_10.5541:1-3539 changes to pilon.changes
            [pilon] Writing updated Contig_826_10.5541_pilon to pilon.fasta
            [pilon] Writing Contig_827_9.10927:1-743 changes to pilon.changes
            [pilon] Writing updated Contig_827_9.10927_pilon to pilon.fasta
            [pilon] Writing Contig_828_9.19011:1-2387 changes to pilon.changes
            [pilon] Writing updated Contig_828_9.19011_pilon to pilon.fasta
            [pilon] Writing Contig_829_9.19254:1-2674 changes to pilon.changes
            [pilon] Writing updated Contig_829_9.19254_pilon to pilon.fasta
            [pilon] Writing Contig_830_7.2665:1-1611 changes to pilon.changes
            [pilon] Writing updated Contig_830_7.2665_pilon to pilon.fasta
            [pilon] Writing Contig_831_8.56341:1-9940 changes to pilon.changes
            [pilon] Writing updated Contig_831_8.56341_pilon to pilon.fasta
            [pilon] Writing Contig_832_8.10397:1-2261 changes to pilon.changes
            [pilon] Writing updated Contig_832_8.10397_pilon to pilon.fasta
            [pilon] Writing Contig_833_8.14432:1-1676 changes to pilon.changes
            [pilon] Writing updated Contig_833_8.14432_pilon to pilon.fasta
            [pilon] Writing Contig_834_6.83474:1-1206 changes to pilon.changes
            [pilon] Writing updated Contig_834_6.83474_pilon to pilon.fasta
            [pilon] Writing Contig_835_10.0411:1-2014 changes to pilon.changes
            [pilon] Writing updated Contig_835_10.0411_pilon to pilon.fasta
            [pilon] Writing Contig_836_8.8792:1-2131 changes to pilon.changes
            [pilon] Writing updated Contig_836_8.8792_pilon to pilon.fasta
            [pilon] Writing Contig_837_7.19271:1-2215 changes to pilon.changes
            [pilon] Writing updated Contig_837_7.19271_pilon to pilon.fasta
            [pilon] Writing Contig_838_9.31579:1-628 changes to pilon.changes
            [pilon] Writing updated Contig_838_9.31579_pilon to pilon.fasta
            [pilon] Writing Contig_839_10.1615:1-8425 changes to pilon.changes
            [pilon] Writing updated Contig_839_10.1615_pilon to pilon.fasta
            [pilon] Writing Contig_840_7.21438:1-799 changes to pilon.changes
            [pilon] Writing updated Contig_840_7.21438_pilon to pilon.fasta
            [pilon] Writing Contig_841_8.95016:1-5156 changes to pilon.changes
            [pilon] Writing updated Contig_841_8.95016_pilon to pilon.fasta
            [pilon] Writing Contig_842_8.9297:1-2481 changes to pilon.changes
            [pilon] Writing updated Contig_842_8.9297_pilon to pilon.fasta
            [pilon] Writing Contig_843_10.0077:1-2730 changes to pilon.changes
            [pilon] Writing updated Contig_843_10.0077_pilon to pilon.fasta
            [pilon] Writing Contig_844_10.0076:1-2133 changes to pilon.changes
            [pilon] Writing updated Contig_844_10.0076_pilon to pilon.fasta
            [pilon] Writing Contig_845_7.77135:1-1730 changes to pilon.changes
            [pilon] Writing updated Contig_845_7.77135_pilon to pilon.fasta
            [pilon] Writing Contig_846_9.0549:1-3317 changes to pilon.changes
            [pilon] Writing updated Contig_846_9.0549_pilon to pilon.fasta
            [pilon] Writing Contig_847_10.056:1-6003 changes to pilon.changes
            [pilon] Writing updated Contig_847_10.056_pilon to pilon.fasta
            [pilon] Writing Contig_848_10.8307:1-4095 changes to pilon.changes
            [pilon] Writing updated Contig_848_10.8307_pilon to pilon.fasta
            [pilon] Writing Contig_849_9.93328:1-10032 changes to pilon.changes
            [pilon] Writing updated Contig_849_9.93328_pilon to pilon.fasta
            [pilon] Writing Contig_850_7.10307:1-1291 changes to pilon.changes
            [pilon] Writing updated Contig_850_7.10307_pilon to pilon.fasta
            [pilon] Writing Contig_851_9.32138:1-3200 changes to pilon.changes
            [pilon] Writing updated Contig_851_9.32138_pilon to pilon.fasta
            [pilon] Writing Contig_852_7.29945:1-4909 changes to pilon.changes
            [pilon] Writing updated Contig_852_7.29945_pilon to pilon.fasta
            [pilon] Writing Contig_853_9.22982:1-1073 changes to pilon.changes
            [pilon] Writing updated Contig_853_9.22982_pilon to pilon.fasta
            [pilon] Writing Contig_854_9.73606:1-1293 changes to pilon.changes
            [pilon] Writing updated Contig_854_9.73606_pilon to pilon.fasta
            [pilon] Writing Contig_855_7.95747:1-4628 changes to pilon.changes
            [pilon] Writing updated Contig_855_7.95747_pilon to pilon.fasta
            [pilon] Writing Contig_856_12.4328:1-958 changes to pilon.changes
            [pilon] Writing updated Contig_856_12.4328_pilon to pilon.fasta
            [pilon] Writing Contig_857_8.88822:1-852 changes to pilon.changes
            [pilon] Writing updated Contig_857_8.88822_pilon to pilon.fasta
            [pilon] Writing Contig_858_7.39547:1-2139 changes to pilon.changes
            [pilon] Writing updated Contig_858_7.39547_pilon to pilon.fasta
            [pilon] Writing Contig_859_16.5209:1-1024 changes to pilon.changes
            [pilon] Writing updated Contig_859_16.5209_pilon to pilon.fasta
            [pilon] Writing Contig_860_9.0718:1-12736 changes to pilon.changes
            [pilon] Writing updated Contig_860_9.0718_pilon to pilon.fasta
            [pilon] Writing Contig_861_7.50187:1-2156 changes to pilon.changes
            [pilon] Writing updated Contig_861_7.50187_pilon to pilon.fasta
            [pilon] Writing Contig_862_8.767:1-5226 changes to pilon.changes
            [pilon] Writing updated Contig_862_8.767_pilon to pilon.fasta
            [pilon] Writing Contig_863_10.2672:1-3373 changes to pilon.changes
            [pilon] Writing updated Contig_863_10.2672_pilon to pilon.fasta
            [pilon] Writing Contig_864_8.93031:1-1168 changes to pilon.changes
            [pilon] Writing updated Contig_864_8.93031_pilon to pilon.fasta
            [pilon] Writing Contig_865_11.6806:1-1889 changes to pilon.changes
            [pilon] Writing updated Contig_865_11.6806_pilon to pilon.fasta
            [pilon] Writing Contig_866_10.5515:1-6551 changes to pilon.changes
            [pilon] Writing updated Contig_866_10.5515_pilon to pilon.fasta
            [pilon] Writing Contig_867_10.34:1-5088 changes to pilon.changes
            [pilon] Writing updated Contig_867_10.34_pilon to pilon.fasta
            [pilon] Writing Contig_868_7.79101:1-3379 changes to pilon.changes
            [pilon] Writing updated Contig_868_7.79101_pilon to pilon.fasta
            [pilon] Writing Contig_869_8.30537:1-4156 changes to pilon.changes
            [pilon] Writing updated Contig_869_8.30537_pilon to pilon.fasta
            [pilon] Writing Contig_870_8.88462:1-618 changes to pilon.changes
            [pilon] Writing updated Contig_870_8.88462_pilon to pilon.fasta
            [pilon] Writing Contig_871_9.03816:1-2326 changes to pilon.changes
            [pilon] Writing updated Contig_871_9.03816_pilon to pilon.fasta
            [pilon] Writing Contig_872_9.26955:1-2053 changes to pilon.changes
            [pilon] Writing updated Contig_872_9.26955_pilon to pilon.fasta
            [pilon] Writing Contig_873_9.37781:1-7193 changes to pilon.changes
            [pilon] Writing updated Contig_873_9.37781_pilon to pilon.fasta
            [pilon] Writing Contig_874_11.3789:1-1300 changes to pilon.changes
            [pilon] Writing updated Contig_874_11.3789_pilon to pilon.fasta
            [pilon] Writing Contig_875_9.48721:1-10925 changes to pilon.changes
            [pilon] Writing updated Contig_875_9.48721_pilon to pilon.fasta
            [pilon] Writing Contig_876_10.3519:1-2492 changes to pilon.changes
            [pilon] Writing updated Contig_876_10.3519_pilon to pilon.fasta
            [pilon] Writing Contig_877_9.83539:1-1806 changes to pilon.changes
            [pilon] Writing updated Contig_877_9.83539_pilon to pilon.fasta
            [pilon] Writing Contig_878_7.47304:1-6622 changes to pilon.changes
            [pilon] Writing updated Contig_878_7.47304_pilon to pilon.fasta
            [pilon] Writing Contig_879_10.1044:1-949 changes to pilon.changes
            [pilon] Writing updated Contig_879_10.1044_pilon to pilon.fasta
            [pilon] Writing Contig_880_8.27419:1-1384 changes to pilon.changes
            [pilon] Writing updated Contig_880_8.27419_pilon to pilon.fasta
            [pilon] Writing Contig_881_9.72433:1-5991 changes to pilon.changes
            [pilon] Writing updated Contig_881_9.72433_pilon to pilon.fasta
            [pilon] Writing Contig_882_9.86064:1-9865 changes to pilon.changes
            [pilon] Writing updated Contig_882_9.86064_pilon to pilon.fasta
            [pilon] Writing Contig_883_7.7491:1-578 changes to pilon.changes
            [pilon] Writing updated Contig_883_7.7491_pilon to pilon.fasta
            [pilon] Writing Contig_884_8.87702:1-1939 changes to pilon.changes
            [pilon] Writing updated Contig_884_8.87702_pilon to pilon.fasta
            [pilon] Writing Contig_885_6.42743:1-647 changes to pilon.changes
            [pilon] Writing updated Contig_885_6.42743_pilon to pilon.fasta
            [pilon] Writing Contig_886_8.94097:1-3493 changes to pilon.changes
            [pilon] Writing updated Contig_886_8.94097_pilon to pilon.fasta
            [pilon] Writing Contig_887_9.02356:1-1081 changes to pilon.changes
            [pilon] Writing updated Contig_887_9.02356_pilon to pilon.fasta
            [pilon] Writing Contig_888_10.558:1-1210 changes to pilon.changes
            [pilon] Writing updated Contig_888_10.558_pilon to pilon.fasta
            [pilon] Writing Contig_889_9.34533:1-2603 changes to pilon.changes
            [pilon] Writing updated Contig_889_9.34533_pilon to pilon.fasta
            [pilon] Writing Contig_890_11.6961:1-2343 changes to pilon.changes
            [pilon] Writing updated Contig_890_11.6961_pilon to pilon.fasta
            [pilon] Writing Contig_891_10.1342:1-1175 changes to pilon.changes
            [pilon] Writing updated Contig_891_10.1342_pilon to pilon.fasta
            [pilon] Writing Contig_892_8.22394:1-2092 changes to pilon.changes
            [pilon] Writing updated Contig_892_8.22394_pilon to pilon.fasta
            [pilon] Writing Contig_893_9.04458:1-7220 changes to pilon.changes
            [pilon] Writing updated Contig_893_9.04458_pilon to pilon.fasta
            [pilon] Writing Contig_894_8.81787:1-3210 changes to pilon.changes
            [pilon] Writing updated Contig_894_8.81787_pilon to pilon.fasta
            [pilon] Writing Contig_895_8.99271:1-4273 changes to pilon.changes
            [pilon] Writing updated Contig_895_8.99271_pilon to pilon.fasta
            [pilon] Writing Contig_896_8.72053:1-2353 changes to pilon.changes
            [pilon] Writing updated Contig_896_8.72053_pilon to pilon.fasta
            [pilon] Writing Contig_897_8.36499:1-6264 changes to pilon.changes
            [pilon] Writing updated Contig_897_8.36499_pilon to pilon.fasta
            [pilon] Writing Contig_898_10.1902:1-7317 changes to pilon.changes
            [pilon] Writing updated Contig_898_10.1902_pilon to pilon.fasta
            [pilon] Writing Contig_899_9.26125:1-1287 changes to pilon.changes
            [pilon] Writing updated Contig_899_9.26125_pilon to pilon.fasta
            [pilon] Writing Contig_900_21.8072:1-2946 changes to pilon.changes
            [pilon] Writing updated Contig_900_21.8072_pilon to pilon.fasta
            [pilon] Writing Contig_901_20.1984:1-2847 changes to pilon.changes
            [pilon] Writing updated Contig_901_20.1984_pilon to pilon.fasta
            [pilon] Writing Contig_902_9.32388:1-5664 changes to pilon.changes
            [pilon] Writing updated Contig_902_9.32388_pilon to pilon.fasta
            [pilon] Writing Contig_903_5.80038:1-2670 changes to pilon.changes
            [pilon] Writing updated Contig_903_5.80038_pilon to pilon.fasta
            [pilon] Writing Contig_904_9.3477:1-10414 changes to pilon.changes
            [pilon] Writing updated Contig_904_9.3477_pilon to pilon.fasta
            [pilon] Writing Contig_905_8.97709:1-762 changes to pilon.changes
            [pilon] Writing updated Contig_905_8.97709_pilon to pilon.fasta
            [pilon] Writing Contig_906_9.28166:1-2555 changes to pilon.changes
            [pilon] Writing updated Contig_906_9.28166_pilon to pilon.fasta
            [pilon] Writing Contig_907_10.067:1-1513 changes to pilon.changes
            [pilon] Writing updated Contig_907_10.067_pilon to pilon.fasta
            [pilon] Writing Contig_908_7.75465:1-1524 changes to pilon.changes
            [pilon] Writing updated Contig_908_7.75465_pilon to pilon.fasta
            [pilon] Writing Contig_909_8.10395:1-1059 changes to pilon.changes
            [pilon] Writing updated Contig_909_8.10395_pilon to pilon.fasta
            [pilon] Mean frags coverage: 17
            [pilon] Mean total coverage: 17
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastqsanger.gz"
            __workflow_invocation_uuid__	"aa5eddbe38ac11f1b6277ced8d8066a8"
            adv	{"depth": "100", "gsize": "", "keep_files": {"__current_case__": 1, "keepfiles": true, "nocorr": "yes_correction"}, "kmers": "", "mincov": "2", "minlen": "0", "namefmt": "contig%05d", "opts": ""}
            assembler	"skesa"
            chromInfo	"/tmp/tmp_5geeevs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            library	{"R1": {"values": [{"id": 1, "src": "hda"}]}, "R2": {"values": [{"id": 2, "src": "hda"}]}, "__current_case__": 0, "lib_type": "paired"}
            log	true
            trim	false

    • Step 4: Bandage contig graph stats (toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bandage_ng:2022.09--h60d1f2b_4

          Command Line:

          • ln -s '/tmp/tmp_5geeevs/files/5/5/6/dataset_556a2824-4c8d-43d6-a546-a0ab39ac4894.dat' input.gfa &&  export QT_QPA_PLATFORM='offscreen' && Bandage info input.gfa  | sed 's/:\s\+/:\t/g' > out.tab

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"aa5eddbe38ac11f1b6277ced8d8066a8"
            chromInfo	"/tmp/tmp_5geeevs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            tsv	false

    • Step 5: Bandage contig graph plot (toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/bandage_ng:2022.09--h60d1f2b_4

          Command Line:

          • ln -s '/tmp/tmp_5geeevs/files/5/5/6/dataset_556a2824-4c8d-43d6-a546-a0ab39ac4894.dat' input.gfa &&  export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.svg' --height '1000' --width '1000'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"aa5eddbe38ac11f1b6277ced8d8066a8"
            chromInfo	"/tmp/tmp_5geeevs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fontsize	None
            height	"1000"
            lengths	false
            names	false
            nodewidth	None
            output_format	"svg"
            width	"1000"

    • Step 6: ToolDistillator (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.4+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/tooldistillator:1.0.4--pyh7e72e81_0

          Command Line:

          • set -x pipefail;  mkdir "tooldistillator_folder" &&   tooldistillator shovill --hid '4' '/tmp/tmp_5geeevs/files/a/9/2/dataset_a92144b0-25f4-48ef-8a5f-27141349749d.dat' --analysis_software_version '1.1.0+galaxy2' --reference_database_version '' -o 'tooldistillator_folder/shovill_0_output.json' | tee 'XXXX'

          Exit Code:

          • 0

          Standard Error:

          • + mkdir tooldistillator_folder
            + tooldistillator shovill --hid 4 /tmp/tmp_5geeevs/files/a/9/2/dataset_a92144b0-25f4-48ef-8a5f-27141349749d.dat --analysis_software_version 1.1.0+galaxy2 --reference_database_version '' -o tooldistillator_folder/shovill_0_output.json
            + tee XXXX
            04/15/2026 09:26:45 AM: interfaces.py: Treatment of /tmp/tmp_5geeevs/files/a/9/2/dataset_a92144b0-25f4-48ef-8a5f-27141349749d.dat
            04/15/2026 09:26:45 AM: interfaces.py: No information for contig_graph_path: Not analyzed
            04/15/2026 09:26:45 AM: interfaces.py: No information for bam_file_path: Not analyzed
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"aa5eddbe38ac11f1b6277ced8d8066a8"
            chromInfo	"/tmp/tmp_5geeevs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            log	false
            tool_section	{"tools": [{"__index__": 0, "select_tool": {"__current_case__": 36, "bam_file_path": null, "contig_graph_path": null, "input": {"values": [{"id": 4, "src": "hda"}]}, "origin": {"__current_case__": 1, "origin": "false"}, "reference_database_version": null, "tool_list": "shovill"}}]}

    • Step 7: ToolDistillator summarize (toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.4+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/tooldistillator:1.0.4--pyh7e72e81_0

          Command Line:

          • tooldistillator --version && mkdir -p input_files && cp '/tmp/tmp_5geeevs/files/4/2/9/dataset_42938c3d-5e20-4271-87be-19182fc71ab3.dat' ./input_files/ && tooldistillator summarize input_files/* -o summary.json

          Exit Code:

          • 0

          Standard Output:

          • tooldistillator 1.0.4
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"aa5eddbe38ac11f1b6277ced8d8066a8"
            chromInfo	"/tmp/tmp_5geeevs/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

  • Other invocation details

    • history_id

      • a1d7e40758524cdc

    • history_state

      • ok

    • invocation_id

      • a1d7e40758524cdc

    • invocation_state

      • scheduled

    • workflow_id

      • a1d7e40758524cdc

[mvdbeek]

Can you isolate the problem and post a bug report at https://github.com/galaxyproject/galaxy/issues ? This seems rather unfortunate