{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/21","repository_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda","labels_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/21/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/21/events","html_url":"https://github.com/PacificBiosciences/pbbioconda/issues/21","id":363911737,"node_id":"MDU6SXNzdWUzNjM5MTE3Mzc=","number":21,"title":"Error at the 4-quiver step of pb-assembly","user":{"login":"a-velt","id":23554476,"node_id":"MDQ6VXNlcjIzNTU0NDc2","avatar_url":"https://avatars0.githubusercontent.com/u/23554476?v=4","gravatar_id":"","url":"https://api.github.com/users/a-velt","html_url":"https://github.com/a-velt","followers_url":"https://api.github.com/users/a-velt/followers","following_url":"https://api.github.com/users/a-velt/following{/other_user}","gists_url":"https://api.github.com/users/a-velt/gists{/gist_id}","starred_url":"https://api.github.com/users/a-velt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-velt/subscriptions","organizations_url":"https://api.github.com/users/a-velt/orgs","repos_url":"https://api.github.com/users/a-velt/repos","events_url":"https://api.github.com/users/a-velt/events{/privacy}","received_events_url":"https://api.github.com/users/a-velt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-09-26T08:26:01Z","updated_at":"2018-09-27T07:12:32Z","closed_at":null,"author_association":"NONE","body":"**Operating system**\r\nLinux 2.6.32-696.16.1.el6.x86_64 - Scientific Linux release 6.9 (Carbon)\r\n\r\n**Package name**\r\nI installed the last version of pb-assembly (version 0.0.0) with conda. I have a bug with fc_quiver.py script.\r\n\r\n**Conda environment**\r\n\r\n```\r\n# packages in environment at /cm/shared/apps/FALCON_12_09_2018:\r\n#\r\n# Name                    Version                   Build  Channel\r\nasn1crypto                0.24.0                   py27_0\r\navro                      1.8.0                    py27_0    bioconda\r\nbcftools                  1.9                  h4da6232_0    bioconda\r\nblas                      1.0                         mkl\r\nblasr                     5.3.2                hac9d22c_3    bioconda\r\nblasr_libcpp              5.3.1                hac9d22c_2    bioconda\r\nbzip2                     1.0.6                h470a237_2    conda-forge\r\nca-certificates           2018.8.24            ha4d7672_0    conda-forge\r\ncertifi                   2018.8.24                py27_1    conda-forge\r\ncffi                      1.11.5           py27he75722e_1\r\nchardet                   3.0.4                    py27_1\r\nconda                     4.5.11                   py27_0    conda-forge\r\nconda-env                 2.6.0                         1\r\ncryptography              2.3.1            py27hc365091_0\r\ncurl                      7.61.0               h93b3f91_2    conda-forge\r\ncython                    0.28.5           py27hfc679d8_0    conda-forge\r\ndecorator                 4.3.0                      py_0    conda-forge\r\nenum34                    1.1.6                    py27_1\r\nfuture                    0.16.0                   py27_2    conda-forge\r\nfutures                   3.2.0                    py27_0\r\ngenomicconsensus          2.3.2                    py27_1    bioconda\r\nh5py                      2.8.0            py27hb794570_1    conda-forge\r\nhdf5                      1.10.2               hc401514_2    conda-forge\r\nhtslib                    1.7                           0    bioconda\r\nidna                      2.7                      py27_0\r\nintel-openmp              2018.0.3                      0\r\nipaddress                 1.0.22                   py27_0\r\niso8601                   0.1.12                     py_1    conda-forge\r\nkrb5                      1.14.6                        0    conda-forge\r\nlibdeflate                1.0                  h470a237_0    bioconda\r\nlibedit                   3.1.20170329         h6b74fdf_2\r\nlibffi                    3.2.1                hd88cf55_4\r\nlibgcc                    7.2.0                h69d50b8_2    conda-forge\r\nlibgcc-ng                 8.2.0                hdf63c60_1\r\nlibgfortran               3.0.0                         1    conda-forge\r\nlibgfortran-ng            7.2.0                hdf63c60_3    conda-forge\r\nlibssh2                   1.8.0                h5b517e9_2    conda-forge\r\nlibstdcxx-ng              8.2.0                hdf63c60_1\r\nlinecache2                1.0.0                    py27_0    conda-forge\r\nminimap2                  2.12                 ha92aebf_0    bioconda\r\nmkl                       2018.0.3                      1\r\nmkl_fft                   1.0.6                    py27_0    conda-forge\r\nmkl_random                1.0.1                    py27_0    conda-forge\r\nmummer                    3.23                    pl526_6    bioconda\r\nncurses                   6.1                  hf484d3e_0\r\nnetworkx                  2.1                        py_1    conda-forge\r\nnim-falcon                0.0.0                         0    bioconda\r\nnumpy                     1.15.1           py27h1d66e8a_0\r\nnumpy-base                1.15.1           py27h81de0dd_0\r\nopenssl                   1.0.2p               h470a237_0    conda-forge\r\npb-assembly               0.0.0                    py27_3    bioconda\r\npb-dazzler                0.0.0                h470a237_0    bioconda\r\npb-falcon                 0.0.2                    py27_0    bioconda\r\npbalign                   0.3.1                    py27_0    bioconda\r\npbbam                     0.18.0               h1310cd9_1    bioconda\r\npbcommand                 1.1.1            py27h24bf2e0_1    bioconda\r\npbcore                    1.5.1                    py27_1    bioconda\r\nperl                      5.26.2               h470a237_0    conda-forge\r\npip                       10.0.1                   py27_0\r\npycosat                   0.6.3            py27h14c3975_0\r\npycparser                 2.18                     py27_1\r\npyopenssl                 18.0.0                   py27_0\r\npysam                     0.14.1           py27hae42fb6_1    bioconda\r\npysocks                   1.6.8                    py27_0\r\npython                    2.7.15               h1571d57_0\r\npython-consensuscore      1.1.1            py27h02d93b8_1    bioconda\r\npython-consensuscore2     3.1.0                    py27_1    bioconda\r\npython-edlib              1.2.3            py27h470a237_1    bioconda\r\npython-intervaltree       2.1.0                      py_0    bioconda\r\npython-msgpack            0.5.6            py27h470a237_0    bioconda\r\npython-sortedcontainers   2.0.4                      py_0    bioconda\r\npytz                      2018.5                     py_0    conda-forge\r\nreadline                  7.0                  h7b6447c_5\r\nrequests                  2.19.1                   py27_0\r\nruamel_yaml               0.15.46          py27h14c3975_0\r\nsamtools                  1.9                  h8ee4bcc_1    bioconda\r\nsetuptools                40.2.0                   py27_0\r\nsix                       1.11.0                   py27_1\r\nsqlite                    3.24.0               h84994c4_0\r\ntk                        8.6.8                hbc83047_0\r\ntraceback2                1.4.0                    py27_0    conda-forge\r\nunittest2                 1.1.0                      py_0    conda-forge\r\nurllib3                   1.23                     py27_0\r\nwheel                     0.31.1                   py27_0\r\nxz                        5.2.4                h470a237_1    conda-forge\r\nyaml                      0.1.7                had09818_2\r\nzlib                      1.2.11               ha838bed_2\r\n```\r\n\r\n**Describe the bug**\r\n\r\nThe step \"3-unzip\" of pb-assembly works well, with the files \"all_p_ctg.fa\" and \"all_h_ctg.fa\" generated, but quiver step doesn't work. I have the impression that it is having an error at the end. Have you ever met this?\r\n\r\nHere the folder 4-quiver. The last step that has worked seems to be quiver-run : \r\n<img width=\"164\" alt=\"quiver\" src=\"https://user-images.githubusercontent.com/23554476/46000932-49354000-c0aa-11e8-84d4-6dfc7e5e001e.PNG\">\r\n\r\nThere are 2639 folders in quiver-run, so there are steps that have worked, but not all.\r\n\r\n**Error message**\r\n\r\nHere the log with the error : \r\n```\r\n [INFO]Popen: 'bash -C /cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pwatcher/mains/job_start.sh >| /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/run-P11ad2b39cd9e4b.bash\r\n .stdout 2>| /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/run-P11ad2b39cd9e4b.bash.stderr'\r\n [ERROR]Task Node(4-quiver/quiver-run/000153Fp01_00001) failed with exit-code=1\r\n [ERROR]Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000153Fp01_00001)])\r\n [ERROR]ready: set([Node(4-quiver/quiver-run/001238Fp01_00002), Node(4-quiver/quiver-run/000889Fp01), Node(4-quiver/quiver-run/000200Fp01), Node(4-quiver/quiver-run/002254Fp02), Node(4-quiver/quiver-run/001827\r\n Fp01), Node(4-quiver/quiver-run/000342Fp01), Node(4-quiver/quiver-run/000474Fp01), Node(4-quiver/quiver-run/000078Fp01_00001), Node(4-quiver/quiver-run/001592Fp01_00001), Node(4-quiver/quiver-run/001250Fp01),\r\n  Node(4-quiver/quiver-run/000682Fp01), Node(4-quiver/quiver-run/001979Fp01), Node(4-quiver/quiver-run/001033Fp01_00001), Node(4-quiver/quiver-run/000477Fp01), Node(4-quiver/quiver-run/000495Fp01), Node(4-quiv\r\n er/quiver-run/002699Fp01), Node(4-quiver/quiver-run/000450Fp01_00001), Node(4-quiver/quiver-run/001441Fp01), Node(4-quiver/quiver-run/000209Fp01), Node(4-quiver/quiver-run/000584Fp01_00001), Node(4-quiver/qui\r\n ...................\r\n ver-run/000645Fp01), Node(4-quiver/quiver-run/000637Fp01), Node(4-quiver/quiver-run/000408Fp01_00003), Node(4-quiver/quiver-run/000176Fp01_00001), Node(4-quiver/quiver-run/002065Fp01), Node(4-quiver/quiver-ru\r\n n/000405Fp01_00002), Node(4-quiver/quiver-run/000675Fp01_00001), Node(4-quiver/quiver-run/000735Fp01_00001), Node(4-quiver/quiver-run/002196Fp02), Node(4-quiver/quiver-run/000743Fp01), Node(4-quiver/quiver-ru\r\n n/000559Fp01_00001), Node(4-quiver/quiver-run/000317Fp01_00002)])\r\n         submitted: set([Node(4-quiver/quiver-run/000484Fp01_00001)])\r\n [ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.\r\n Traceback (most recent call last):\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/bin//fc_quiver.py\", line 11, in <module>\r\n     load_entry_point('falcon-unzip==1.1.2', 'console_scripts', 'fc_quiver.py')()\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_unzip/mains/start_unzip.py\", line 29, in main\r\n     unzip.run(**vars(args))\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_unzip/unzip.py\", line 126, in run\r\n     unzip_all(config)\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_unzip/unzip.py\", line 28, in unzip_all\r\n     tasks_unzip.run_workflow(wf, config, rule_writer)\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_unzip/tasks/unzip.py\", line 708, in run_workflow\r\n    job_dict=config['job.step.unzip.quiver'],\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_kit/pype.py\", line 192, in gen_parallel_tasks\r\n     wf.refreshTargets()\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py\", line 277, in refreshTargets\r\n     self._refreshTargets(updateFreq, exitOnFailure)\r\n   File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py\", line 361, in _refreshTargets\r\n     raise Exception(msg)\r\nException: Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000153Fp01_00001)])\r\nmake: *** [quiver] Error 1\r\n```\r\n\r\nHere the \"4-quiver/quiver-run/000153Fp01_00001/run-P11ad2b39cd9e4b.bash.stderr\" file : \r\n\r\n```\r\nexecutable=${PYPEFLOW_JOB_START_SCRIPT}\r\n+ executable=/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/run-P11ad2b39cd9e4b.bash\r\ntimeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default\r\n+ timeout=60\r\n\r\n# Wait up to timeout seconds for the executable to become \"executable\",\r\n# then exec.\r\n#timeleft = int(timeout)\r\nwhile [[ ! -x \"${executable}\" ]]; do\r\n    if [[ \"${timeout}\" == \"0\" ]]; then\r\n        echo \"timed out waiting for (${executable})\"\r\n        exit 77\r\n    fi\r\n    echo \"not executable: '${executable}', waiting ${timeout}s\"\r\n    sleep 1\r\n    timeout=$((timeout-1))\r\ndone\r\n+ [[ ! -x /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/run-P11ad2b39cd9e4b.bash ]]\r\n\r\n/bin/bash ${executable}\r\n+ /bin/bash /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/run-P11ad2b39cd9e4b.bash\r\n+ '[' '!' -d /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001 ']'\r\n+ cd /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001\r\n+ eval '/bin/bash run.sh'\r\n++ /bin/bash run.sh\r\nexport PATH=$PATH:/bin\r\n+ export PATH=/cm/shared/apps/FALCON_12_09_2018/bin/:/cm/shared/apps/Perl_conda/bin:/cm/shared/apps/slurm/14.03.0/sbin:/cm/shared/apps/slurm/14.03.0/bin:/cm/local/apps/cluster-tools/bin:/cm/local/apps/cmd/sbi\r\nn:/cm/local/apps/cmd/bin:/cm/shared/apps/cmgui:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/dell/srvadmin/bin:/opt/dell/srvadmin/sbin:/root/bin:/bin\r\n+ PATH=/cm/shared/apps/FALCON_12_09_2018/bin/:/cm/shared/apps/Perl_conda/bin:/cm/shared/apps/slurm/14.03.0/sbin:/cm/shared/apps/slurm/14.03.0/bin:/cm/local/apps/cluster-tools/bin:/cm/local/apps/cmd/sbin:/cm/l\r\nocal/apps/cmd/bin:/cm/shared/apps/cmgui:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/dell/srvadmin/bin:/opt/dell/srvadmin/sbin:/root/bin:/bin\r\ncd /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001\r\n+ cd /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001\r\n/bin/bash task.sh\r\n+ /bin/bash task.sh\r\npypeflow 2.0.4\r\n2018-09-25 01:34:24,412 - root - DEBUG - Running \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/task.js\r\non\"\r\n2018-09-25 01:34:24,414 - root - DEBUG - Checking existence of '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/task.json' with timeout=30\r\n2018-09-25 01:34:24,414 - root - DEBUG - Loading JSON from '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001/task.json'\r\n2018-09-25 01:34:24,415 - root - DEBUG - {u'bash_template_fn': u'template.sh',\r\n u'inputs': {u'bash_template': u'/data2/avelt/Assembly_amurensis/4-quiver/quiver-split/bash-template.sh',\r\n             u'units_of_work': u'/data2/avelt/Assembly_amurensis/4-quiver/quiver-chunks/000153Fp01_00001/some-units-of-work.json'},\r\n u'outputs': {u'results': u'results.json'},\r\n u'parameters': {u'pypeflow_mb': 4000, u'pypeflow_nproc': u'5'}}\r\n2018-09-25 01:34:24,415 - root - WARNING - CD: '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001' <- '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001'\r\n2018-09-25 01:34:24,415 - root - DEBUG - Checking existence of u'/data2/avelt/Assembly_amurensis/4-quiver/quiver-chunks/000153Fp01_00001/some-units-of-work.json' with timeout=30\r\n2018-09-25 01:34:24,416 - root - DEBUG - Checking existence of u'/data2/avelt/Assembly_amurensis/4-quiver/quiver-split/bash-template.sh' with timeout=30\r\n2018-09-25 01:34:24,416 - root - DEBUG - Checking existence of u'template.sh' with timeout=30\r\n2018-09-25 01:34:24,416 - root - WARNING - CD: '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001' <- '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001'\r\n2018-09-25 01:34:24,417 - root - INFO - $('/bin/bash user_script.sh')\r\nhostname\r\n+ hostname\r\npwd\r\n+ pwd\r\ndate\r\n+ date\r\n# Substitution will be similar to snakemake \"shell\".\r\npython -m falcon_kit.mains.generic_run_units_of_work --nproc=5 --units-of-work-fn=/data2/avelt/Assembly_amurensis/4-quiver/quiver-chunks/000153Fp01_00001/some-units-of-work.json --bash-template-fn=/data2/avel\r\nt/Assembly_amurensis/4-quiver/quiver-split/bash-template.sh --results-fn=results.json\r\n+ python -m falcon_kit.mains.generic_run_units_of_work --nproc=5 --units-of-work-fn=/data2/avelt/Assembly_amurensis/4-quiver/quiver-chunks/000153Fp01_00001/some-units-of-work.json --bash-template-fn=/data2/av\r\nelt/Assembly_amurensis/4-quiver/quiver-split/bash-template.sh --results-fn=results.json\r\nfalcon-kit 1.2.2\r\npypeflow 2.0.4\r\nINFO:root:INPUT:{u'ref_fasta': u'/data2/avelt/Assembly_amurensis/4-quiver/quiver-split/./refs/000153Fp01_00001/ref.fa', u'read_bam': u'/data2/avelt/Assembly_amurensis/4-quiver/segregate-run/segr1905/segregate\r\nd/000153Fp01_00001/000153Fp01_00001.bam', u'ctg_type': u'/data2/avelt/Assembly_amurensis/4-quiver/quiver-split/./refs/000153Fp01_00001/ctg_type'}\r\nINFO:root:OUTPUT:{u'cns_fasta': u'cns.fasta.gz', u'cns_vcf': u'cns.vcf', u'job_done': u'quiver_done', u'ctg_type_again': u'ctg_type', u'cns_fastq': u'cns.fastq.gz'}\r\nINFO:root:PARAMS:{'pypeflow_nproc': '5', u'ctg_id': u'000153Fp01_00001'}\r\nINFO:root:$('rm -rf uow-00')\r\nWARNING:root:CD: 'uow-00' <- '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001'\r\nINFO:root:$('/bin/bash user_script.sh')\r\nhostname\r\n+ hostname\r\npwd\r\n+ pwd\r\ndate\r\n+ date\r\nset -vex\r\n+ set -vex\r\ntrap 'touch quiver_done.exit' EXIT\r\n+ trap 'touch quiver_done.exit' EXIT\r\nhostname\r\n+ hostname\r\ndate\r\n+ date\r\n\r\nsamtools faidx /data2/avelt/Assembly_amurensis/4-quiver/quiver-split/./refs/000153Fp01_00001/ref.fa\r\n+ samtools faidx /data2/avelt/Assembly_amurensis/4-quiver/quiver-split/./refs/000153Fp01_00001/ref.fa\r\n[faidx] Could not build fai index /data2/avelt/Assembly_amurensis/4-quiver/quiver-split/./refs/000153Fp01_00001/ref.fa.fai\r\ntouch quiver_done.exit\r\n+ touch quiver_done.exit\r\nWARNING:root:Call '/bin/bash user_script.sh' returned 256.\r\nWARNING:root:CD: 'uow-00' -> '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001'\r\nTraceback (most recent call last):\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/runpy.py\", line 174, in _run_module_as_main\r\n    \"__main__\", fname, loader, pkg_name)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/runpy.py\", line 72, in _run_code\r\n    exec code in run_globals\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py\", line 115, in <module>\r\n    main()\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py\", line 111, in main\r\n    run(**vars(args))\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/falcon_kit/mains/generic_run_units_of_work.py\", line 64, in run\r\n    pypeflow.do_task.run_bash(script, inputs, outputs, params)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py\", line 178, in run_bash\r\n    util.system(cmd)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/io.py\", line 29, in syscall\r\n    raise Exception(msg)\r\nException: Call '/bin/bash user_script.sh' returned 256.\r\n2018-09-25 01:34:24,870 - root - WARNING - Call '/bin/bash user_script.sh' returned 256.\r\n2018-09-25 01:34:24,870 - root - WARNING - CD: '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001' -> '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001'\r\n2018-09-25 01:34:24,870 - root - WARNING - CD: '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001' -> '/data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001'\r\n2018-09-25 01:34:24,870 - root - CRITICAL - Error in /cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py with args=\"{'json_fn': '/data2/avelt/Assembly_amurensis/4-quiver/quiver-r\r\nun/000153Fp01_00001/task.json',\\n 'timeout': 30,\\n 'tmpdir': None}\"\r\nTraceback (most recent call last):\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/runpy.py\", line 174, in _run_module_as_main\r\n    \"__main__\", fname, loader, pkg_name)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/runpy.py\", line 72, in _run_code\r\n    exec code in run_globals\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py\", line 246, in <module>\r\n    main()\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py\", line 238, in main\r\n    run(**vars(parsed_args))\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py\", line 232, in run\r\n    run_cfg_in_tmpdir(cfg, tmpdir)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py\", line 208, in run_cfg_in_tmpdir\r\n    run_bash(bash_template, myinputs, myoutputs, parameters)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/do_task.py\", line 178, in run_bash\r\n    util.system(cmd)\r\n  File \"/cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pypeflow/io.py\", line 29, in syscall\r\n    raise Exception(msg)\r\nException: Call '/bin/bash user_script.sh' returned 256.\r\n+++ pwd\r\n++ echo 'FAILURE. Running top in /data2/avelt/Assembly_amurensis/4-quiver/quiver-run/000153Fp01_00001 (If you see -terminal database is inaccessible- you are using the python bin-wrapper, so you will not get\r\ndiagnostic info. No big deal. This process is crashing anyway.)'\r\n++ rm -f top.txt\r\n++ which python\r\n++ which top\r\n++ env -u LD_LIBRARY_PATH top -b -n 1\r\n++ env -u LD_LIBRARY_PATH top -b -n 1\r\n++ pstree -apl\r\n\r\nreal    0m1.432s\r\nuser    0m0.327s\r\nsys     0m0.164s\r\n+ finish\r\n+ echo 'finish code: 1'\r\n\r\n```\r\n\r\n**To Reproduce**\r\nI give you the two fasta files at the end of the 3-unzip step, are they enough?\r\nhttps://www.dropbox.com/s/l5n2gu2etdhkute/3-unzip.zip?dl=0\r\n\r\n**Expected behavior**\r\nI expect that two polished fasta files must be generate, one for primary contigs and one for haplotigs.\r\n\r\nBest,\r\nAmandine"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/comments/424983281","html_url":"https://github.com/PacificBiosciences/pbbioconda/issues/21#issuecomment-424983281","issue_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/21","id":424983281,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNDk4MzI4MQ==","user":{"login":"a-velt","id":23554476,"node_id":"MDQ6VXNlcjIzNTU0NDc2","avatar_url":"https://avatars0.githubusercontent.com/u/23554476?v=4","gravatar_id":"","url":"https://api.github.com/users/a-velt","html_url":"https://github.com/a-velt","followers_url":"https://api.github.com/users/a-velt/followers","following_url":"https://api.github.com/users/a-velt/following{/other_user}","gists_url":"https://api.github.com/users/a-velt/gists{/gist_id}","starred_url":"https://api.github.com/users/a-velt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-velt/subscriptions","organizations_url":"https://api.github.com/users/a-velt/orgs","repos_url":"https://api.github.com/users/a-velt/repos","events_url":"https://api.github.com/users/a-velt/events{/privacy}","received_events_url":"https://api.github.com/users/a-velt/received_events","type":"User","site_admin":false},"created_at":"2018-09-27T07:12:32Z","updated_at":"2018-09-27T07:12:32Z","author_association":"NONE","body":"Hi,\r\n\r\nThank you for your help. There is juste the header in the ref.fa file : \r\n`more /data2/avelt/Assembly_amurensis/4-quiver/quiver-split/./refs/000153Fp01_00001/ref.fa`\r\n\r\n`>000153Fp01_00001`\r\n\r\nI launched: \r\n`conda update pb-assembly`\r\n\r\nAnd now the conda list : \r\n```\r\n# packages in environment at /cm/shared/apps/FALCON_12_09_2018:\r\n#\r\n# Name                    Version                   Build  Channel\r\nasn1crypto                0.24.0                   py27_0\r\navro                      1.8.0                    py27_0    bioconda\r\nbcftools                  1.9                  h4da6232_0    bioconda\r\nbedtools                  2.27.1               he941832_2    bioconda\r\nblas                      1.0                         mkl\r\nblasr                     5.3.2                hac9d22c_3    bioconda\r\nblasr_libcpp              5.3.1                hac9d22c_2    bioconda\r\nbwa                       0.7.17               ha92aebf_3    bioconda\r\nbzip2                     1.0.6                h470a237_2    conda-forge\r\nca-certificates           2018.8.24            ha4d7672_0    conda-forge\r\ncertifi                   2018.8.24             py27_1001    conda-forge\r\ncffi                      1.11.5           py27he75722e_1\r\nchardet                   3.0.4                    py27_1\r\nconda                     4.5.11                   py27_0    conda-forge\r\nconda-env                 2.6.0                         1\r\ncryptography              2.3.1            py27hc365091_0\r\ncurl                      7.61.0               h93b3f91_2    conda-forge\r\ncython                    0.28.5           py27hfc679d8_0    conda-forge\r\ndecorator                 4.3.0                      py_0    conda-forge\r\nenum34                    1.1.6                    py27_1\r\nfuture                    0.16.0                   py27_2    conda-forge\r\nfutures                   3.2.0                    py27_0\r\ngenomicconsensus          2.3.2                    py27_1    bioconda\r\nh5py                      2.8.0            py27hb794570_1    conda-forge\r\nhdf5                      1.10.2               hc401514_2    conda-forge\r\nhtslib                    1.7                           0    bioconda\r\nidna                      2.7                      py27_0\r\nintel-openmp              2018.0.3                      0\r\nipaddress                 1.0.22                   py27_0\r\niso8601                   0.1.12                     py_1    conda-forge\r\nkrb5                      1.14.6                        0    conda-forge\r\nlibdeflate                1.0                  h470a237_0    bioconda\r\nlibedit                   3.1.20170329         h6b74fdf_2\r\nlibffi                    3.2.1                hd88cf55_4\r\nlibgcc                    7.2.0                h69d50b8_2    conda-forge\r\nlibgcc-ng                 8.2.0                hdf63c60_1\r\nlibgfortran               3.0.0                         1    conda-forge\r\nlibgfortran-ng            7.2.0                hdf63c60_3    conda-forge\r\nlibssh2                   1.8.0                h5b517e9_2    conda-forge\r\nlibstdcxx-ng              8.2.0                hdf63c60_1\r\nlinecache2                1.0.0                    py27_0    conda-forge\r\nminimap2                  2.12                 ha92aebf_0    bioconda\r\nmkl                       2018.0.3                      1\r\nmkl_fft                   1.0.6                    py27_0    conda-forge\r\nmkl_random                1.0.1                    py27_0    conda-forge\r\nmummer                    3.23                    pl526_6    bioconda\r\nmummer4                   4.0.0beta2      pl526hfc679d8_3    bioconda\r\nncurses                   6.1                  hf484d3e_0\r\nnetworkx                  2.1                        py_1    conda-forge\r\nnim-falcon                0.0.0                         0    bioconda\r\nnumpy                     1.15.1           py27h1d66e8a_0\r\nnumpy-base                1.15.1           py27h81de0dd_0\r\nopenssl                   1.0.2p               h470a237_0    conda-forge\r\npb-assembly               0.0.1                    py27_0    bioconda\r\npb-dazzler                0.0.0                h470a237_0    bioconda\r\npb-falcon                 0.2.3            py27ha92aebf_0    bioconda\r\npbalign                   0.3.1                    py27_0    bioconda\r\npbbam                     0.18.0               h1310cd9_1    bioconda\r\npbcommand                 1.1.1            py27h24bf2e0_1    bioconda\r\npbcore                    1.5.1                    py27_1    bioconda\r\nperl                      5.26.2               h470a237_0    conda-forge\r\npip                       10.0.1                   py27_0\r\npycosat                   0.6.3            py27h14c3975_0\r\npycparser                 2.18                     py27_1\r\npyopenssl                 18.0.0                   py27_0\r\npysam                     0.14.1           py27hae42fb6_1    bioconda\r\npysocks                   1.6.8                    py27_0\r\npython                    2.7.15               h1571d57_0\r\npython-consensuscore      1.1.1            py27h02d93b8_1    bioconda\r\npython-consensuscore2     3.1.0                    py27_1    bioconda\r\npython-edlib              1.2.3            py27h470a237_1    bioconda\r\npython-intervaltree       2.1.0                      py_0    bioconda\r\npython-msgpack            0.5.6            py27h470a237_0    bioconda\r\npython-sortedcontainers   2.0.4                      py_0    bioconda\r\npytz                      2018.5                     py_0    conda-forge\r\nreadline                  7.0                  h7b6447c_5\r\nrequests                  2.19.1                   py27_0\r\nruamel_yaml               0.15.46          py27h14c3975_0\r\nsamtools                  1.9                  h8ee4bcc_1    bioconda\r\nsetuptools                40.2.0                   py27_0\r\nsix                       1.11.0                   py27_1\r\nsqlite                    3.24.0               h84994c4_0\r\ntk                        8.6.8                hbc83047_0\r\ntraceback2                1.4.0                    py27_0    conda-forge\r\nunittest2                 1.1.0                      py_0    conda-forge\r\nurllib3                   1.23                     py27_0\r\nwheel                     0.31.1                   py27_0\r\nxz                        5.2.4                h470a237_1    conda-forge\r\nyaml                      0.1.7                had09818_2\r\nzlib                      1.2.11               ha838bed_2\r\n```\r\n\r\nI will launch the 4-quiver step with the new version of pb-assembly/pb-falcon. I will keep you in touch.\r\n\r\nBest,\r\nAmandine"}}
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