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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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Failure in generate_haplotigs_for_ctg((u'000519F', u'../../0-phasing/000519F/uow-00/proto', './uow-000519F', u'../../..', False)) #31

Closed jinshui0202 closed 5 years ago

jinshui0202 commented 6 years ago 
executable=${PYPEFLOW_JOB_START_SCRIPT}
+ executable=/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/run-Pda9cd060b80965.bash
timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default
+ timeout=60

# Wait up to timeout seconds for the executable to become "executable",
# then exec.
#timeleft = int(timeout)
while [[ ! -x "${executable}" ]]; do
    if [[ "${timeout}" == "0" ]]; then
        echo "timed out waiting for (${executable})"
        exit 77
    fi
    echo "not executable: '${executable}', waiting ${timeout}s"
    sleep 1
    timeout=$((timeout-1))
done
+ [[ ! -x /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/run-Pda9cd060b80965.bash ]]

/bin/bash ${executable}
+ /bin/bash /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/run-Pda9cd060b80965.bash
+ '[' '!' -d /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F ']'
+ cd /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F
+ eval '/bin/bash run.sh'
++ /bin/bash run.sh
export PATH=$PATH:/bin
+ export PATH=/home/mskkk/.pyenv/versions/anaconda-2.0.0/bin:/home/mskkk/.pyenv/libexec:/home/mskkk/.pyenv/plugins/python-build/bin:/home/mskkk/.pyenv/shims:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/home/mskkk/tools/RepeatMasker:/home/mskkk/tools/GARM_v0.7.5:/home/mskkk/tools/RepeatScout-1:/home/mskkk/tools/tophat-2.1.0.Linux_x86_64:/home/mskkk/tools/cufflinks-2.2.1.Linux_x86_64:/home/mskkk/tools/RECON1.05/bin:/home/mskkk/tools/biocode/lib:/home/mskkk/tools/RepeatModeler:/home/mskkk/tools/pigz-2.3.3:/home/mskkk/tools/canu-1.6/Linux-amd64/bin:/home/mskkk/tools/mugsy_x86-64-v1r2.2:/home/mskkk/tools/PhaME/bin:/home/mskkk/tools/paml4.8/src:/home/mskkk/tools/angsd:/home/mskkk/tools/mpj/bin:/home/mskkk/tools/hmmer-3.1b2-linux-intel-x86_64/binaries:/home/mskkk/tools/PILER/home/mskkk/tools/OMA/OMA/bin:/home/mskkk/tools/BRAKER1:/home/mskkk/tools/PhiPack/src/home/mskkk/toolsAxML:/home/mskkk/tools/phylip-3.696/exe:/home/mskkk/tools/bowtie2-2.2.5/:/home/mskkk/tools/geneid/bin:/home/mskkk/tools/wise-2.4.1/src/bin:/home/mskkk/tools/CEGMA_v2.5/bin:/home/mskkk/tools/bwa-0.7.12:/home/mskkk/smrtanalysis/install/smrtanalysis_2.3.0.140936/smrtcmds/bin:/home/mskkk/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin:/home/mskkk/tools/MEGA7:/home/mskkk/tools/SPAdes-3.9.1-Linux/bin:/home/mskkk/tools/apache-maven-3.3.9/bin:/home/mskkk/tools/MetaCRAST/bin:/home/mskkk/tools/ClonalFrameML/src:/home/mskkk/toolsAxML:/home/mskkk/bin:/home/mskkk/tools/picard/dist:/home/mskkk/tools/PBSuite_15.8.24//bin:/home/mskkk/tools/picard-tools-2.1.0:/home/mskkk/tools/art:/home/mskkk/tools/soap.coverage:/home/mskkk/tools/soap2.21release:/home/mskkk/tools/NxTrim:/home/mskkk/tools/circos-0.69/bin:/home/mskkk/tools/anaconda2/bin:/home/mskkk/tools/bbmap:/home/mskkk/tools/OMA/OMA/bin:/home/mskkk/tools/pIRS_111:/home/mskkk/.pyenv/bin:/home/mskkk/toolsoary/bin:/usr/local/gcc-5.4/bin:/home/mskkk/toolsacon/tools/graphmap/bin/Linux-x64:/home/mskkk/toolsacon/tools/minimap:/home/mskkk/toolsacon/tools/edlib/src:/home/mskkk/toolsacon/scripts:/home/mskkk/toolsacon/bin:/home/mskkk/tools/miniasm:/home/mskkk/tools/pitchfork/deployment/bin:/home/mskkk/tools/DBG2OLC:/home/mskkk/tools/quickmerge/merger:/home/mskkk/tools/MaSuRCA-3.2.2_RC1/bin:/home/mskkk/tools/MECAT/Linux-amd64/bin:/home/mskkk/tools/sratoolkit.2.8.2-1-centos_linux64/bin:/home/mskkk/tools/wtdbg:/home/mskkk/tools/HaploMerger2_20161205/bin:/home/mskkk/tools/HaploMerger2_20161205/chainNet_jksrc20100603_centOS6:/home/mskkk/bin/x86_64-redhat-linux-gnu:/home/mskkk/tools/DEXTRACTOR:/home/mskkk/hhf/soft/MUMmer3.23/:/home/mskkk/hhf/soft/centrifuge-1.0.3-beta:/home/mskkk/hhf/soft/ANIcalculator_v1:/home/mskkk/hhf/soft/pplacer-Linux-v1.1.alpha19:/home/mskkk/hhf/soft/FragGeneScan1.30:/home/mskkk/tools/bin:/home/mskkk/tools/mash-Linux64-v1.1.1:/home/mskkk/hhf/soft/minced:/home/mskkk/tools/pitchfork/deployment/bin:/home/mskkk/tools/smrtanalysis/install/smrtlink-release_5.0.1.9585/bundles/smrttools/install/smrttools-release_5.0.1.9578/smrtcmds/bin:/home/mskkk/hhf/soft:/home/mskkk/tools/prokka-1.11/bin:/home/mskkk/tools/FastME-master-09a5862b5a227724b0d034dc33b6f1bf802cfb99/src:/home/mskkk/miniconda3/bin:/home/mskkk/tools/minimap:/home/mskkk/tools/signalp-4.1:/home/mskkk/tools/Roary/bin:/home/mskkk/msq/homer/bin:/home/mskkk/test2/test2/blastx/primer/primer3-2.4.0/src:/home/mskkk/tools/snippy/bin:/home/mskkk/tools/autoANI/scripts/edirect:/home/mskkk/tools/pplacer-Darwin-v1.1.alpha17-6-g5cecf99:/home/mskkk/tools/harvesttools-Linux64-v1.2:/home/mskkk/tools/pplacer-Linux-v1.1.alpha17:/home/mskkk/tools/cdhit:/home/mskkk/tools/nim-0.18.0/bin:/home/mskkk/tools/Roary/bin:/home/mskkk/tools/FALCON-Phase/bin:/home/mskkk/.local/bin:/home/mskkk/bin:/home/mskkk/msq/HI-C/tools/samtools-0.1.19:/home/mskkk/tools/maker/bin:/home/mskkk/hhf/soft/Mash/bin:/home/mskkk/hhf/soft/ANIcalculator_v1:/bin
+ PATH=/home/mskkk/.pyenv/versions/anaconda-2.0.0/bin:/home/mskkk/.pyenv/libexec:/home/mskkk/.pyenv/plugins/python-build/bin:/home/mskkk/.pyenv/shims:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/home/mskkk/tools/RepeatMasker:/home/mskkk/tools/GARM_v0.7.5:/home/mskkk/tools/RepeatScout-1:/home/mskkk/tools/tophat-2.1.0.Linux_x86_64:/home/mskkk/tools/cufflinks-2.2.1.Linux_x86_64:/home/mskkk/tools/RECON1.05/bin:/home/mskkk/tools/biocode/lib:/home/mskkk/tools/RepeatModeler:/home/mskkk/tools/pigz-2.3.3:/home/mskkk/tools/canu-1.6/Linux-amd64/bin:/home/mskkk/tools/mugsy_x86-64-v1r2.2:/home/mskkk/tools/PhaME/bin:/home/mskkk/tools/paml4.8/src:/home/mskkk/tools/angsd:/home/mskkk/tools/mpj/bin:/home/mskkk/tools/hmmer-3.1b2-linux-intel-x86_64/binaries:/home/mskkk/tools/PILER/home/mskkk/tools/OMA/OMA/bin:/home/mskkk/tools/BRAKER1:/home/mskkk/tools/PhiPack/src/home/mskkk/toolsAxML:/home/mskkk/tools/phylip-3.696/exe:/home/mskkk/tools/bowtie2-2.2.5/:/home/mskkk/tools/geneid/bin:/home/mskkk/tools/wise-2.4.1/src/bin:/home/mskkk/tools/CEGMA_v2.5/bin:/home/mskkk/tools/bwa-0.7.12:/home/mskkk/smrtanalysis/install/smrtanalysis_2.3.0.140936/smrtcmds/bin:/home/mskkk/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/bin:/home/mskkk/tools/MEGA7:/home/mskkk/tools/SPAdes-3.9.1-Linux/bin:/home/mskkk/tools/apache-maven-3.3.9/bin:/home/mskkk/tools/MetaCRAST/bin:/home/mskkk/tools/ClonalFrameML/src:/home/mskkk/toolsAxML:/home/mskkk/bin:/home/mskkk/tools/picard/dist:/home/mskkk/tools/PBSuite_15.8.24//bin:/home/mskkk/tools/picard-tools-2.1.0:/home/mskkk/tools/art:/home/mskkk/tools/soap.coverage:/home/mskkk/tools/soap2.21release:/home/mskkk/tools/NxTrim:/home/mskkk/tools/circos-0.69/bin:/home/mskkk/tools/anaconda2/bin:/home/mskkk/tools/bbmap:/home/mskkk/tools/OMA/OMA/bin:/home/mskkk/tools/pIRS_111:/home/mskkk/.pyenv/bin:/home/mskkk/toolsoary/bin:/usr/local/gcc-5.4/bin:/home/mskkk/toolsacon/tools/graphmap/bin/Linux-x64:/home/mskkk/toolsacon/tools/minimap:/home/mskkk/toolsacon/tools/edlib/src:/home/mskkk/toolsacon/scripts:/home/mskkk/toolsacon/bin:/home/mskkk/tools/miniasm:/home/mskkk/tools/pitchfork/deployment/bin:/home/mskkk/tools/DBG2OLC:/home/mskkk/tools/quickmerge/merger:/home/mskkk/tools/MaSuRCA-3.2.2_RC1/bin:/home/mskkk/tools/MECAT/Linux-amd64/bin:/home/mskkk/tools/sratoolkit.2.8.2-1-centos_linux64/bin:/home/mskkk/tools/wtdbg:/home/mskkk/tools/HaploMerger2_20161205/bin:/home/mskkk/tools/HaploMerger2_20161205/chainNet_jksrc20100603_centOS6:/home/mskkk/bin/x86_64-redhat-linux-gnu:/home/mskkk/tools/DEXTRACTOR:/home/mskkk/hhf/soft/MUMmer3.23/:/home/mskkk/hhf/soft/centrifuge-1.0.3-beta:/home/mskkk/hhf/soft/ANIcalculator_v1:/home/mskkk/hhf/soft/pplacer-Linux-v1.1.alpha19:/home/mskkk/hhf/soft/FragGeneScan1.30:/home/mskkk/tools/bin:/home/mskkk/tools/mash-Linux64-v1.1.1:/home/mskkk/hhf/soft/minced:/home/mskkk/tools/pitchfork/deployment/bin:/home/mskkk/tools/smrtanalysis/install/smrtlink-release_5.0.1.9585/bundles/smrttools/install/smrttools-release_5.0.1.9578/smrtcmds/bin:/home/mskkk/hhf/soft:/home/mskkk/tools/prokka-1.11/bin:/home/mskkk/tools/FastME-master-09a5862b5a227724b0d034dc33b6f1bf802cfb99/src:/home/mskkk/miniconda3/bin:/home/mskkk/tools/minimap:/home/mskkk/tools/signalp-4.1:/home/mskkk/tools/Roary/bin:/home/mskkk/msq/homer/bin:/home/mskkk/test2/test2/blastx/primer/primer3-2.4.0/src:/home/mskkk/tools/snippy/bin:/home/mskkk/tools/autoANI/scripts/edirect:/home/mskkk/tools/pplacer-Darwin-v1.1.alpha17-6-g5cecf99:/home/mskkk/tools/harvesttools-Linux64-v1.2:/home/mskkk/tools/pplacer-Linux-v1.1.alpha17:/home/mskkk/tools/cdhit:/home/mskkk/tools/nim-0.18.0/bin:/home/mskkk/tools/Roary/bin:/home/mskkk/tools/FALCON-Phase/bin:/home/mskkk/.local/bin:/home/mskkk/bin:/home/mskkk/msq/HI-C/tools/samtools-0.1.19:/home/mskkk/tools/maker/bin:/home/mskkk/hhf/soft/Mash/bin:/home/mskkk/hhf/soft/ANIcalculator_v1:/bin
cd /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F
+ cd /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F
/bin/bash task.sh
+ /bin/bash task.sh
pypeflow 2.1.0
2018-09-30 09:11:08,309 - root - DEBUG - Running "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/task.json"
2018-09-30 09:11:08,310 - root - DEBUG - Checking existence of '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/task.json' with timeout=30
2018-09-30 09:11:08,310 - root - DEBUG - Loading JSON from '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/task.json'
2018-09-30 09:11:08,311 - root - DEBUG - {u'bash_template_fn': u'template.sh',
 u'inputs': {u'bash_template': u'../split/dummy.sh',
             u'units_of_work': u'../chunks/chunk_000519F/some-units-of-work.json'},
 u'outputs': {u'results': u'result-list.json'},
 u'parameters': {u'pypeflow_mb': u'131072', u'pypeflow_nproc': u'16'}}
2018-09-30 09:11:08,311 - root - WARNING - CD: '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F' <- '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F'
2018-09-30 09:11:08,311 - root - DEBUG - Checking existence of u'../chunks/chunk_000519F/some-units-of-work.json' with timeout=30
2018-09-30 09:11:08,311 - root - DEBUG - Checking existence of u'../split/dummy.sh' with timeout=30
2018-09-30 09:11:08,311 - root - DEBUG - Checking existence of u'template.sh' with timeout=30
2018-09-30 09:11:08,311 - root - WARNING - CD: '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F' <- '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F'
2018-09-30 09:11:08,312 - root - INFO - $('/bin/bash user_script.sh')
hostname
+ hostname
pwd
+ pwd
date
+ date
# Substitution will be similar to snakemake "shell".
    python -m falcon_unzip.mains.graphs_to_h_tigs_2 apply --units-of-work-fn=../chunks/chunk_000519F/some-units-of-work.json --results-fn=result-list.json
+ python -m falcon_unzip.mains.graphs_to_h_tigs_2 apply --units-of-work-fn=../chunks/chunk_000519F/some-units-of-work.json --results-fn=result-list.json
falcon-unzip 1.1.3
falcon-kit 1.2.3
pypeflow 2.1.0
[INFO 2018-09-30 09:11:09] Loading units-of-work from '../chunks/chunk_000519F/some-units-of-work.json'
[INFO 2018-09-30 09:11:09] Loading p assembly graph.
[INFO 2018-09-30 09:11:09] Counting 22,425,424 bytes from
  "../../../2-asm-falcon/sg_edges_list"
[INFO 2018-09-30 09:11:09]         #1 count=             61   0.00% 
[INFO 2018-09-30 09:11:09]         #3 count=            182   0.00% 
[INFO 2018-09-30 09:11:09]         #6 count=            363   0.00% 
[INFO 2018-09-30 09:11:09]        #10 count=            607   0.00% 
[INFO 2018-09-30 09:11:09]        #19 count=          1,153   0.01% 
[INFO 2018-09-30 09:11:09]        #36 count=          2,188   0.01% 
[INFO 2018-09-30 09:11:09]        #69 count=          4,190   0.02% 
[INFO 2018-09-30 09:11:09]       #134 count=          8,133   0.04% 
[INFO 2018-09-30 09:11:09]       #263 count=         15,967   0.07% 
[INFO 2018-09-30 09:11:09]       #521 count=         31,636   0.14% 
[INFO 2018-09-30 09:11:09]     #1,036 count=         62,921   0.28% 
[INFO 2018-09-30 09:11:09]     #2,065 count=        125,438   0.56% 
[INFO 2018-09-30 09:11:09]     #4,122 count=        250,399   1.12% 
[INFO 2018-09-30 09:11:09]     #8,236 count=        500,312   2.23% 
[INFO 2018-09-30 09:11:09]    #16,463 count=      1,000,061   4.46% 
[INFO 2018-09-30 09:11:09]    #32,914 count=      1,999,516   8.92% 
[INFO 2018-09-30 09:11:09]    #65,819 count=      3,998,394  17.83% 
[INFO 2018-09-30 09:11:09]   #102,734 count=      6,240,954  27.83% 
[INFO 2018-09-30 09:11:10]   #139,650 count=      8,483,539  37.83% 
[INFO 2018-09-30 09:11:10]   #176,567 count=     10,726,131  47.83% 
[INFO 2018-09-30 09:11:10]   #213,484 count=     12,968,692  57.83% 
[INFO 2018-09-30 09:11:11]   #250,399 count=     15,211,263  67.83% 
[INFO 2018-09-30 09:11:11]   #287,318 count=     17,453,864  77.83% 
[INFO 2018-09-30 09:11:11]   #324,233 count=     19,696,413  87.83% 
[INFO 2018-09-30 09:11:11]   #361,149 count=     21,938,970  97.83% 
[INFO 2018-09-30 09:11:12]   #369,156 count=     22,425,424 100.00% 
[INFO 2018-09-30 09:11:12] Counting 2,915,868 bytes from
  "../../../2-asm-falcon/utg_data"
[INFO 2018-09-30 09:11:12]         #1 count=             81   0.00% 
[INFO 2018-09-30 09:11:12]         #2 count=            236   0.01% 
[INFO 2018-09-30 09:11:12]         #4 count=            457   0.02% 
[INFO 2018-09-30 09:11:12]         #7 count=            813   0.03% 
[INFO 2018-09-30 09:11:12]        #14 count=          1,493   0.05% 
[INFO 2018-09-30 09:11:12]        #25 count=          2,835   0.10% 
[INFO 2018-09-30 09:11:12]        #49 count=          6,040   0.21% 
[INFO 2018-09-30 09:11:12]        #89 count=         11,320   0.39% 
[INFO 2018-09-30 09:11:12]       #172 count=         21,761   0.75% 
[INFO 2018-09-30 09:11:12]       #342 count=         42,574   1.46% 
[INFO 2018-09-30 09:11:12]       #679 count=         84,132   2.89% 
[INFO 2018-09-30 09:11:12]     #1,347 count=        167,122   5.73% 
[INFO 2018-09-30 09:11:12]     #2,636 count=        333,338  11.43% 
[INFO 2018-09-30 09:11:12]     #4,954 count=        624,928  21.43% 
[INFO 2018-09-30 09:11:12]     #7,242 count=        916,628  31.44% 
[INFO 2018-09-30 09:11:12]     #9,524 count=      1,208,363  41.44% 
[INFO 2018-09-30 09:11:12]    #11,839 count=      1,500,080  51.45% 
[INFO 2018-09-30 09:11:12]    #14,143 count=      1,791,737  61.45% 
[INFO 2018-09-30 09:11:12]    #16,456 count=      2,083,390  71.45% 
[INFO 2018-09-30 09:11:12]    #18,718 count=      2,375,127  81.46% 
[INFO 2018-09-30 09:11:12]    #21,037 count=      2,666,803  91.46% 
[INFO 2018-09-30 09:11:12]    #23,012 count=      2,915,868 100.00% 
[INFO 2018-09-30 09:11:12] Counting 346,781 bytes from
  "../../../2-asm-falcon/ctg_paths"
[INFO 2018-09-30 09:11:12]         #1 count=          4,008   1.16% 
[INFO 2018-09-30 09:11:12]         #3 count=         10,197   2.94% 
[INFO 2018-09-30 09:11:12]         #7 count=         19,380   5.59% 
[INFO 2018-09-30 09:11:12]        #14 count=         35,547  10.25% 
[INFO 2018-09-30 09:11:12]        #32 count=         68,262  19.68% 
[INFO 2018-09-30 09:11:12]        #56 count=        103,225  29.77% 
[INFO 2018-09-30 09:11:12]        #92 count=        138,720  40.00% 
[INFO 2018-09-30 09:11:12]       #145 count=        173,915  50.15% 
[INFO 2018-09-30 09:11:12]       #220 count=        208,670  60.17% 
[INFO 2018-09-30 09:11:12]       #347 count=        243,379  70.18% 
[INFO 2018-09-30 09:11:12]       #523 count=        278,145  80.21% 
[INFO 2018-09-30 09:11:12]       #777 count=        312,902  90.23% 
[INFO 2018-09-30 09:11:12]     #1,050 count=        346,781 100.00% 
[INFO 2018-09-30 09:11:14] Loading h assembly graph.
[INFO 2018-09-30 09:11:14] Counting 9,768,957 bytes from
  "../../1-hasm/sg_edges_list"
[INFO 2018-09-30 09:11:14]         #1 count=             60   0.00% 
[INFO 2018-09-30 09:11:14]         #2 count=            120   0.00% 
[INFO 2018-09-30 09:11:14]         #5 count=            295   0.00% 
[INFO 2018-09-30 09:11:14]        #10 count=            584   0.01% 
[INFO 2018-09-30 09:11:14]        #19 count=          1,099   0.01% 
[INFO 2018-09-30 09:11:14]        #36 count=          2,085   0.02% 
[INFO 2018-09-30 09:11:14]        #70 count=          4,050   0.04% 
[INFO 2018-09-30 09:11:14]       #136 count=          7,903   0.08% 
[INFO 2018-09-30 09:11:14]       #269 count=         15,616   0.16% 
[INFO 2018-09-30 09:11:14]       #534 count=         31,029   0.32% 
[INFO 2018-09-30 09:11:14]     #1,064 count=         61,764   0.63% 
[INFO 2018-09-30 09:11:14]     #2,124 count=        123,262   1.26% 
[INFO 2018-09-30 09:11:14]     #4,243 count=        246,174   2.52% 
[INFO 2018-09-30 09:11:14]     #8,478 count=        491,952   5.04% 
[INFO 2018-09-30 09:11:14]    #16,955 count=        983,481  10.07% 
[INFO 2018-09-30 09:11:14]    #33,798 count=      1,960,383  20.07% 
[INFO 2018-09-30 09:11:14]    #50,650 count=      2,937,328  30.07% 
[INFO 2018-09-30 09:11:14]    #67,488 count=      3,914,262  40.07% 
[INFO 2018-09-30 09:11:14]    #84,337 count=      4,891,187  50.07% 
[INFO 2018-09-30 09:11:14]   #101,186 count=      5,868,114  60.07% 
[INFO 2018-09-30 09:11:14]   #118,032 count=      6,845,037  70.07% 
[INFO 2018-09-30 09:11:15]   #134,888 count=      7,821,977  80.07% 
[INFO 2018-09-30 09:11:15]   #151,740 count=      8,798,917  90.07% 
[INFO 2018-09-30 09:11:15]   #168,478 count=      9,768,957 100.00% 
[INFO 2018-09-30 09:11:15] Counting 1,784,322 bytes from
  "../../1-hasm/utg_data"
[INFO 2018-09-30 09:11:15]         #1 count=            308   0.02% 
[INFO 2018-09-30 09:11:15]         #3 count=            667   0.04% 
[INFO 2018-09-30 09:11:15]        #10 count=          1,366   0.08% 
[INFO 2018-09-30 09:11:15]        #21 count=          2,600   0.15% 
[INFO 2018-09-30 09:11:15]        #42 count=          5,068   0.28% 
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[INFO 2018-09-30 09:11:15]       #178 count=         19,989   1.12% 
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[INFO 2018-09-30 09:11:15]     #2,776 count=        315,848  17.70% 
[INFO 2018-09-30 09:11:15]     #4,343 count=        494,324  27.70% 
[INFO 2018-09-30 09:11:15]     #5,943 count=        673,028  37.72% 
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[INFO 2018-09-30 09:11:15]     #9,066 count=      1,029,917  57.72% 
[INFO 2018-09-30 09:11:15]    #10,669 count=      1,208,376  67.72% 
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[INFO 2018-09-30 09:11:15]    #13,785 count=      1,565,543  87.74% 
[INFO 2018-09-30 09:11:15]    #15,336 count=      1,744,070  97.74% 
[INFO 2018-09-30 09:11:15]    #15,682 count=      1,784,322 100.00% 
[INFO 2018-09-30 09:11:15] Counting 849,964 bytes from
  "../../1-hasm/ctg_paths"
[INFO 2018-09-30 09:11:15]         #1 count=            370   0.04% 
[INFO 2018-09-30 09:11:15]         #2 count=            740   0.09% 
[INFO 2018-09-30 09:11:15]         #4 count=          1,550   0.18% 
[INFO 2018-09-30 09:11:15]        #10 count=          3,255   0.38% 
[INFO 2018-09-30 09:11:15]        #25 count=          6,359   0.75% 
[INFO 2018-09-30 09:11:15]        #53 count=         12,328   1.45% 
[INFO 2018-09-30 09:11:15]       #115 count=         24,406   2.87% 
[INFO 2018-09-30 09:11:15]       #241 count=         48,247   5.68% 
[INFO 2018-09-30 09:11:15]       #531 count=         95,668  11.26% 
[INFO 2018-09-30 09:11:15]     #1,116 count=        180,720  21.26% 
[INFO 2018-09-30 09:11:15]     #1,752 count=        265,757  31.27% 
[INFO 2018-09-30 09:11:15]     #2,408 count=        350,823  41.28% 
[INFO 2018-09-30 09:11:15]     #3,093 count=        435,930  51.29% 
[INFO 2018-09-30 09:11:15]     #3,795 count=        520,991  61.30% 
[INFO 2018-09-30 09:11:15]     #4,514 count=        606,002  71.30% 
[INFO 2018-09-30 09:11:15]     #5,243 count=        691,081  81.31% 
[INFO 2018-09-30 09:11:15]     #5,982 count=        776,120  91.31% 
[INFO 2018-09-30 09:11:15]     #6,628 count=        849,964 100.00% 
[INFO 2018-09-30 09:11:16] Loading phasing info and making the read ID sets.
[INFO 2018-09-30 09:11:16] Counting 9,072,742 bytes from
  "../../1-hasm/concatenated-rid-to-phase/rid_to_phase.all"
[INFO 2018-09-30 09:11:16]         #1 count=             23   0.00% 
[INFO 2018-09-30 09:11:16]         #2 count=             51   0.00% 
[INFO 2018-09-30 09:11:16]         #4 count=            102   0.00% 
[INFO 2018-09-30 09:11:16]         #8 count=            209   0.00% 
[INFO 2018-09-30 09:11:16]        #16 count=            413   0.00% 
[INFO 2018-09-30 09:11:16]        #31 count=            783   0.01% 
[INFO 2018-09-30 09:11:16]        #62 count=          1,531   0.02% 
[INFO 2018-09-30 09:11:16]       #123 count=          3,009   0.03% 
[INFO 2018-09-30 09:11:16]       #242 count=          5,961   0.07% 
[INFO 2018-09-30 09:11:16]       #478 count=         11,849   0.13% 
[INFO 2018-09-30 09:11:16]       #958 count=         23,629   0.26% 
[INFO 2018-09-30 09:11:16]     #1,914 count=         47,192   0.52% 
[INFO 2018-09-30 09:11:17]     #3,809 count=         94,312   1.04% 
[INFO 2018-09-30 09:11:17]     #7,589 count=        188,532   2.08% 
[INFO 2018-09-30 09:11:17]    #15,296 count=        376,964   4.15% 
[INFO 2018-09-30 09:11:17]    #30,389 count=        753,801   8.31% 
[INFO 2018-09-30 09:11:17]    #60,749 count=      1,507,466  16.62% 
[INFO 2018-09-30 09:11:17]    #96,621 count=      2,414,742  26.62% 
[INFO 2018-09-30 09:11:17]   #132,567 count=      3,322,035  36.62% 
[INFO 2018-09-30 09:11:18]   #168,859 count=      4,229,323  46.62% 
[INFO 2018-09-30 09:11:18]   #205,215 count=      5,136,606  56.62% 
[INFO 2018-09-30 09:11:18]   #241,435 count=      6,043,890  66.62% 
[INFO 2018-09-30 09:11:18]   #278,088 count=      6,951,184  76.62% 
[INFO 2018-09-30 09:11:18]   #314,652 count=      7,858,465  86.62% 
[INFO 2018-09-30 09:11:19]   #350,865 count=      8,765,754  96.62% 
[INFO 2018-09-30 09:11:19]   #362,896 count=      9,072,742 100.00% 
[INFO 2018-09-30 09:11:19] Counted 9,072,742 bytes in 362896 calls from:
  "../../1-hasm/concatenated-rid-to-phase/rid_to_phase.all"
[INFO 2018-09-30 09:11:19] Loading the 2-asm-falcon primary contigs.
[INFO 2018-09-30 09:11:19] Counting 220,086,479 bytes from
  "/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/2-asm-falcon/p_ctg.fa"
[INFO 2018-09-30 09:11:19]         #1 count=      5,737,008   2.61% 
[INFO 2018-09-30 09:11:19]         #3 count=     14,315,258   6.50% 
[INFO 2018-09-30 09:11:19]         #7 count=     28,971,807  13.16% 
[INFO 2018-09-30 09:11:19]        #14 count=     51,406,235  23.36% 
[INFO 2018-09-30 09:11:20]        #23 count=     74,898,079  34.03% 
[INFO 2018-09-30 09:11:20]        #34 count=     98,066,774  44.56% 
[INFO 2018-09-30 09:11:20]        #50 count=    120,371,811  54.69% 
[INFO 2018-09-30 09:11:20]        #72 count=    142,768,651  64.87% 
[INFO 2018-09-30 09:11:20]       #103 count=    164,996,177  74.97% 
[INFO 2018-09-30 09:11:20]       #167 count=    187,008,747  84.97% 
[INFO 2018-09-30 09:11:21]       #347 count=    209,047,237  94.98% 
[INFO 2018-09-30 09:11:21] Done loading 2-asm-falcon primary contigs.
[INFO 2018-09-30 09:11:21] Loading tiling paths.
[INFO 2018-09-30 09:11:21] Done loading tiling paths.
[INFO 2018-09-30 09:11:21] Loading the 1-hasm haplotigs.
[INFO 2018-09-30 09:11:22] Counting 254,918,040 bytes from
  "/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/1-hasm/p_ctg.fa"
[INFO 2018-09-30 09:11:22]         #1 count=        326,563   0.13% 
[INFO 2018-09-30 09:11:22]         #2 count=        664,713   0.26% 
[INFO 2018-09-30 09:11:22]         #5 count=      1,594,075   0.63% 
[INFO 2018-09-30 09:11:22]        #10 count=      2,961,522   1.16% 
[INFO 2018-09-30 09:11:22]        #21 count=      5,730,623   2.25% 
[INFO 2018-09-30 09:11:22]        #47 count=     11,040,295   4.33% 
[INFO 2018-09-30 09:11:22]       #106 count=     21,598,454   8.47% 
[INFO 2018-09-30 09:11:22]       #248 count=     42,625,133  16.72% 
[INFO 2018-09-30 09:11:22]       #458 count=     68,203,569  26.76% 
[INFO 2018-09-30 09:11:23]       #703 count=     93,774,277  36.79% 
[INFO 2018-09-30 09:11:23]       #981 count=    119,339,674  46.81% 
[INFO 2018-09-30 09:11:23]     #1,287 count=    144,886,940  56.84% 
[INFO 2018-09-30 09:11:23]     #1,631 count=    170,409,468  66.85% 
[INFO 2018-09-30 09:11:24]     #2,021 count=    195,907,420  76.85% 
[INFO 2018-09-30 09:11:24]     #2,482 count=    221,431,622  86.86% 
[INFO 2018-09-30 09:11:24]     #3,089 count=    246,937,442  96.87% 
[INFO 2018-09-30 09:11:24] Loading haplotigs.
[INFO 2018-09-30 09:11:24] Counting 3,314 units from
  "tiling_paths"
[INFO 2018-09-30 09:11:24]         #1 count=              1   0.03% 000040F-HAP000527F-000040F.1000002.0
[INFO 2018-09-30 09:11:24]         #3 count=              3   0.09% 000092F-HAP000333F-000092F.1000003.0
[INFO 2018-09-30 09:11:24]         #7 count=              7   0.21% 000021F-HAP000547F-000021F.3000004.0
[INFO 2018-09-30 09:11:24]        #15 count=             15   0.45% 000043F-HAP002339F-000043F.3000013.0
[INFO 2018-09-30 09:11:24]        #31 count=             31   0.94% 000008F-HAP002200F-000008F.3000008.1
[INFO 2018-09-30 09:11:24]        #63 count=             63   1.90% 000276F-HAP002571F-000276F.1000002.1
[INFO 2018-09-30 09:11:24]       #127 count=            127   3.83% 000142F-HAP003211F-000142F.3000001.1
[INFO 2018-09-30 09:11:24]       #255 count=            255   7.69% 000003F-HAP002644F-000003F.3000020.0
[INFO 2018-09-30 09:11:24]       #511 count=            511  15.42% 000006F-HAP000472F-000006F.1000014.0
[INFO 2018-09-30 09:11:24]       #842 count=            842  25.41% 000004F-HAP002552F-000004F.3000011.1
[INFO 2018-09-30 09:11:24]     #1,173 count=          1,173  35.40% 000019F-HAP001552F-000019F.1000015.1
[INFO 2018-09-30 09:11:24]     #1,504 count=          1,504  45.38% 000014F-HAP000808F-000014F.1000014.1
[INFO 2018-09-30 09:11:24]     #1,835 count=          1,835  55.37% 000004F-HAP001069F-000004F.5000022.0
[INFO 2018-09-30 09:11:24]     #2,166 count=          2,166  65.36% 000206F-HAP001399F-000206F.1000001.1
[INFO 2018-09-30 09:11:24]     #2,497 count=          2,497  75.35% 000049F-HAP002129F-000049F.3000006.0
[INFO 2018-09-30 09:11:24]     #2,828 count=          2,828  85.33% 000001F-HAP000445F-000001F.7000029.1
[INFO 2018-09-30 09:11:24]     #3,159 count=          3,159  95.32% 000034F-HAP000253F-000034F.1000006.0
[INFO 2018-09-30 09:11:24] Done loading haplotigs.
[INFO 2018-09-30 09:11:24] Loading sg_edges_list.
[INFO 2018-09-30 09:11:24] Counting 9,768,957 bytes from
  "../../1-hasm/sg_edges_list"
[INFO 2018-09-30 09:11:24]         #1 count=             60   0.00% 
[INFO 2018-09-30 09:11:24]         #2 count=            120   0.00% 
[INFO 2018-09-30 09:11:24]         #5 count=            295   0.00% 
[INFO 2018-09-30 09:11:24]        #10 count=            584   0.01% 
[INFO 2018-09-30 09:11:24]        #19 count=          1,099   0.01% 
[INFO 2018-09-30 09:11:24]        #36 count=          2,085   0.02% 
[INFO 2018-09-30 09:11:24]        #70 count=          4,050   0.04% 
[INFO 2018-09-30 09:11:24]       #136 count=          7,903   0.08% 
[INFO 2018-09-30 09:11:24]       #269 count=         15,616   0.16% 
[INFO 2018-09-30 09:11:24]       #534 count=         31,029   0.32% 
[INFO 2018-09-30 09:11:24]     #1,064 count=         61,764   0.63% 
[INFO 2018-09-30 09:11:25]     #2,124 count=        123,262   1.26% 
[INFO 2018-09-30 09:11:25]     #4,243 count=        246,174   2.52% 
[INFO 2018-09-30 09:11:25]     #8,478 count=        491,952   5.04% 
[INFO 2018-09-30 09:11:25]    #16,955 count=        983,481  10.07% 
[INFO 2018-09-30 09:11:25]    #33,798 count=      1,960,383  20.07% 
[INFO 2018-09-30 09:11:25]    #50,650 count=      2,937,328  30.07% 
[INFO 2018-09-30 09:11:25]    #67,488 count=      3,914,262  40.07% 
[INFO 2018-09-30 09:11:25]    #84,337 count=      4,891,187  50.07% 
[INFO 2018-09-30 09:11:25]   #101,186 count=      5,868,114  60.07% 
[INFO 2018-09-30 09:11:25]   #118,032 count=      6,845,037  70.07% 
[INFO 2018-09-30 09:11:25]   #134,888 count=      7,821,977  80.07% 
[INFO 2018-09-30 09:11:26]   #151,740 count=      8,798,917  90.07% 
[INFO 2018-09-30 09:11:26]   #168,478 count=      9,768,957 100.00% 
[INFO 2018-09-30 09:11:26] Counted 9,768,957 bytes in 168478 calls from:
  "../../1-hasm/sg_edges_list"
[INFO 2018-09-30 09:11:26] Done loading sg_edges_list.
[INFO 2018-09-30 09:11:26] Running 1 units of work.
[INFO 2018-09-30 09:11:26] UOW #0 of 1 ...
[INFO 2018-09-30 09:11:26] Entering generate_haplotigs_for_ctg(ctg_id=u'000519F', out_dir='./uow-000519F', base_dir=u'../../..'
[INFO 2018-09-30 09:11:26] New logging FileHandler: '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/uow-000519F/prototype.log'
[INFO 2018-09-30 09:11:26] Started processing contig: "000519F".
[INFO 2018-09-30 09:11:26] Fetching the p_ctg_seq.
[INFO 2018-09-30 09:11:26] Fetching the p_ctg_tiling_path.
[INFO 2018-09-30 09:11:26] Loading minced ctg seqs from u'../../0-phasing/000519F/uow-00/proto/minced.fasta' .
[INFO 2018-09-30 09:11:26] Counting 32,459 bytes from
  "/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/0-phasing/000519F/uow-00/proto/minced.fasta"
[INFO 2018-09-30 09:11:26]         #1 count=         32,458 100.00% 
[INFO 2018-09-30 09:11:26] Loading the phase relation graph from u'../../0-phasing/000519F/uow-00/proto/phase_relation_graph.gexf' .
[INFO 2018-09-30 09:11:26] Loading all regions from u'../../0-phasing/000519F/uow-00/proto/regions.json' .
[INFO 2018-09-30 09:11:26] Making bubble region list.
[INFO 2018-09-30 09:11:26] Retupling.
[INFO 2018-09-30 09:11:26] Assigning sequences to all regions.
[INFO 2018-09-30 09:11:26] Getting snp_haplotigs.
[INFO 2018-09-30 09:11:26] Writing haplotigs to disk: './uow-000519F/aln_snp_hasm_ctg.fasta'
[INFO 2018-09-30 09:11:26] [IS] Writing 1, h_name = 000519F-HAP003071F-000519F.1000001.1
[INFO 2018-09-30 09:11:26] [IS] Writing 2, h_name = 000519F-HAP002320F-000519F.1000001.0
[EXECUTE 2018-09-30 09:11:26] [2018/09/30 01:11:26] Executing "blasr --minMatch 15 --maxMatch 25 --advanceHalf --advanceExactMatches 10 --bestn 1 --nproc 16 --noSplitSubreads ./uow-000519F/aln_snp_hasm_ctg.fasta ../../../3-unzip/reads/000519F/ref.fa --sam --out ./uow-000519F/aln_snp_hasm_ctg.tmp.sam"
[INFO] 2018-09-30T09:11:26 [blasr] started.
[INFO] 2018-09-30T09:11:26 [blasr] ended.
[EXECUTE 2018-09-30 09:11:26] [2018/09/30 01:11:26]  Finished subprocess.
[EXECUTE 2018-09-30 09:11:26] [2018/09/30 01:11:26] Executing "samtools sort ./uow-000519F/aln_snp_hasm_ctg.tmp.sam -o ./uow-000519F/aln_snp_hasm_ctg.sam"
[EXECUTE 2018-09-30 09:11:26] [2018/09/30 01:11:26]  Finished subprocess.
[EXECUTE 2018-09-30 09:11:26] [2018/09/30 01:11:26] Executing "rm -f ./uow-000519F/aln_snp_hasm_ctg.tmp.sam"
[EXECUTE 2018-09-30 09:11:26] [2018/09/30 01:11:26]  Finished subprocess.
[INFO 2018-09-30 09:11:26] Loading the alignments.
[INFO 2018-09-30 09:11:26] Reorienting haplotigs.
[INFO 2018-09-30 09:11:26]   - qname = 000519F-HAP003071F-000519F.1000001.1
[INFO 2018-09-30 09:11:26] 
[INFO 2018-09-30 09:11:26]  start = (0, 642), end = (32435, 33061)
[INFO 2018-09-30 09:11:26] pos_of_interest for q_name: 000519F-HAP003071F-000519F.1000001.1
[INFO 2018-09-30 09:11:26] ((0, 642), (32435, 33061), '000519F-HAP003071F-000519F.1000001.1', 38200, '000519F', 32435, ('000519F', 1000001, 1))
[INFO 2018-09-30 09:11:26] 
[INFO 2018-09-30 09:11:26]  start = (0, 771), end = (32435, 33232)
[INFO 2018-09-30 09:11:26] pos_of_interest for q_name: 000519F-HAP002320F-000519F.1000001.0
[INFO 2018-09-30 09:11:26] ((0, 771), (32435, 33232), '000519F-HAP002320F-000519F.1000001.0', 39550, '000519F', 32435, ('000519F', 1000001, 0))
[INFO 2018-09-30 09:11:26] 
[INFO 2018-09-30 09:11:26] Function: "__main__"
[INFO 2018-09-30 09:11:26] len(sorted_bubble_regions) = 1
[INFO 2018-09-30 09:11:26] Handling prefix.
[INFO 2018-09-30 09:11:26] Entered function: "__main__"
[INFO 2018-09-30 09:11:26] Exiting function: "__main__"
[INFO 2018-09-30 09:11:26] Handling infix.
[INFO 2018-09-30 09:11:26] Handling suffix.
[INFO 2018-09-30 09:11:26] Entered function: "__main__"
[INFO 2018-09-30 09:11:26] Exiting function: "__main__"
[INFO 2018-09-30 09:11:26] Dunn!
[INFO 2018-09-30 09:11:26] Creating a haplotig graph.
[INFO 2018-09-30 09:11:26]   - Adding nodes.
[INFO 2018-09-30 09:11:26]     - region_id = 0, region_type = diploid, region_pos_start = 0, region_pos_end = 32435
[INFO 2018-09-30 09:11:26]       - [haplotig graph, adding node] key = 000519F-HAP003071F-000519F.1000001.1-0
[INFO 2018-09-30 09:11:26]       - [haplotig graph, adding node] key = 000519F-HAP002320F-000519F.1000001.0-0
[INFO 2018-09-30 09:11:26]   - Adding edges.
[INFO 2018-09-30 09:11:26]   - Hashing haplotigs.
[INFO 2018-09-30 09:11:26]   - Writing the haplotig graph in the gexf format.
[INFO 2018-09-30 09:11:26] Writing the haplotig_graph.gfa.
[INFO 2018-09-30 09:11:26]   - Writing all the haplotigs to disk in haplotigs.fasta.
[INFO 2018-09-30 09:11:26] Beginning to extract all p_ctg and h_ctg.
[INFO 2018-09-30 09:11:26] Extracting primary contig: p_ctg_id = 000519F
[INFO 2018-09-30 09:11:26] Making the haplotig segment coordinate relation lookup.
[INFO 2018-09-30 09:11:26] haplotig_segment_coords = {0: 0, 32435: 32419}

[INFO 2018-09-30 09:11:26] Extracting the associate haplotigs for p_ctg_id = 000519F
[ERROR 2018-09-30 09:11:26] Failure in generate_haplotigs_for_ctg((u'000519F', u'../../0-phasing/000519F/uow-00/proto', './uow-000519F', u'../../..', False))
Traceback (most recent call last):
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 74, in run_generate_haplotigs_for_ctg
    return generate_haplotigs_for_ctg(ctg_id, allow_multiple_primaries, out_dir, unzip_dir, proto_dir, logger)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 256, in generate_haplotigs_for_ctg
    extract_and_write_all_ctg(ctg_id, haplotig_graph, all_haplotig_dict, phase_alias_map, out_dir, allow_multiple_primaries, fp_proto_log)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 959, in extract_and_write_all_ctg
    raise Exception(msg)
Exception: Skipping additional subgraphs of the primary contig: 000519F. The graph has multiple primary components.
Traceback (most recent call last):
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 1495, in <module>
    main()
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 1491, in main
    args.func(args)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 1253, in cmd_apply
    result = run_generate_haplotigs_for_ctg(exe)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 74, in run_generate_haplotigs_for_ctg
    return generate_haplotigs_for_ctg(ctg_id, allow_multiple_primaries, out_dir, unzip_dir, proto_dir, logger)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 256, in generate_haplotigs_for_ctg
    extract_and_write_all_ctg(ctg_id, haplotig_graph, all_haplotig_dict, phase_alias_map, out_dir, allow_multiple_primaries, fp_proto_log)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 959, in extract_and_write_all_ctg
    raise Exception(msg)
Exception: Skipping additional subgraphs of the primary contig: 000519F. The graph has multiple primary components.
2018-09-30 09:11:29,257 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.
2018-09-30 09:11:29,258 - root - WARNING - CD: '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F' -> '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F'
2018-09-30 09:11:29,258 - root - WARNING - CD: '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F' -> '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F'
2018-09-30 09:11:29,259 - root - CRITICAL - Error in /home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py with args="{'json_fn': '/public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F/task.json',\n 'timeout': 30,\n 'tmpdir': None}"
Traceback (most recent call last):
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py", line 267, in <module>
    main()
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py", line 259, in main
    run(**vars(parsed_args))
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py", line 253, in run
    run_cfg_in_tmpdir(cfg, tmpdir, '.')
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py", line 228, in run_cfg_in_tmpdir
    run_bash(bash_template, myinputs, myoutputs, parameters)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/do_task.py", line 187, in run_bash
    util.system(cmd)
  File "/home/mskkk/.pyenv/versions/anaconda-2.0.0/lib/python2.7/site-packages/pypeflow/io.py", line 29, in syscall
    raise Exception(msg)
Exception: Call '/bin/bash user_script.sh' returned 256.
+++ pwd
++ echo 'FAILURE. Running top in /public/mskkk/Nematode/Mi/WuhanF4-1/01-assembly/falcon/3-unzip/2-htigs/chunk_000519F (If you see -terminal database is inaccessible- you are using the python bin-wrapper, so you will not get diagnostic info. No big deal. This process is crashing anyway.)'
++ rm -f top.txt
++ which python
++ which top
++ env -u LD_LIBRARY_PATH top -b -n 1
++ env -u LD_LIBRARY_PATH top -b -n 1
++ pstree -apl

real    0m21.948s
user    0m19.299s
sys 0m2.758s
+ finish
+ echo 'finish code: 1'
marcopessoa commented 6 years ago

Same issue here. Exception message states "Exception: Skipping additional subgraphs of the primary contig: XXXXXXX. The graph has multiple primary components."

Subscribing to thread and hoping this gets fixed soon.

marcopessoa commented 5 years ago

Not sure if this could be the cause, but when I ran fc_run for assembly I had falcon-kit 1.2.2 installed. Then I updated pb-assembly, and when running fc_unzip.py I had falcon-kit 1.2.3. I am running a new assembly with falcon-kit 1.2.4 and falcon-unzip 1.1.4 with the same dataset and will check if this happens again.

isovic commented 5 years ago

Hi, Thank you for reporting this issue. We addressed it and it should have been resolved in falcon-unzip 1.1.4 available in pb-falcon>=0.2.4 and pb-assembly>=0.0.2. It looks like you have tried the latest version recently - could you confirm whether it worked for you well?

marcopessoa commented 5 years ago

I got to the polishing step with Arrow, so Unzip worked fine. No issues so far.

isovic commented 5 years ago

Ok, thank you! Closing this issue then. Best regards, Ivan.