{"action":"closed","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1154","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1154/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1154/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1154/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1154","id":121822490,"number":1154,"title":"Error running VarScan on yeast samples","user":{"login":"funnell","id":381464,"avatar_url":"https://avatars.githubusercontent.com/u/381464?v=3","gravatar_id":"","url":"https://api.github.com/users/funnell","html_url":"https://github.com/funnell","followers_url":"https://api.github.com/users/funnell/followers","following_url":"https://api.github.com/users/funnell/following{/other_user}","gists_url":"https://api.github.com/users/funnell/gists{/gist_id}","starred_url":"https://api.github.com/users/funnell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/funnell/subscriptions","organizations_url":"https://api.github.com/users/funnell/orgs","repos_url":"https://api.github.com/users/funnell/repos","events_url":"https://api.github.com/users/funnell/events{/privacy}","received_events_url":"https://api.github.com/users/funnell/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-12-12T01:11:11Z","updated_at":"2016-01-08T00:15:07Z","closed_at":"2016-01-08T00:15:07Z","body":"Running bcbio-nextgen locally in parallel:\r\n```\r\nbcbio_nextgen.py ../config/CX5461_yeast.yaml -t local -n 50 --retries 3\r\n```\r\n\r\nI receive the following errors related to VarScan:\r\n```\r\n[2015-12-10T03:06Z] Genotyping with varscan: ('chrVII', 1084896, 1090940) 47_2015-12-05_CX5461_yeast-sort-chrVII_1084896_1090940-prep.bam\r\n[2015-12-10T03:06Z] mpileup for Varscan\r\n[2015-12-10T03:06Z] [mpileup] 1 samples in 1 input files\r\n[2015-12-10T03:06Z] <mpileup> Set max per-file depth to 8000\r\n[2015-12-10T03:06Z] Uncaught exception occurred\r\nTraceback (most recent call last):\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 21, in run\r\n    _do_run(cmd, checks, log_stdout)\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 95, in _do_run\r\n    raise subprocess.CalledProcessError(exitcode, error_msg)\r\nCalledProcessError: Command 'set -o pipefail; /shahlab/tfunnell/bcbio-nextgen/bin/samtools mpileup -f /shahlab/tfunnell/bcbio-nextgen/genomes/Scerevisiae/sacCer3/seq/sacCer3.fa -d 1000 -L 1000 -r chrVII:1084897-1090940 /shahlab/tfunnell/bcbio_work/CX5461_yeast/work/bamprep/SA779_A51801/chrVII/47_2015-12-05_CX5461_yeast-sort-chrVII_1084896_1090940-prep.bam | grep -v -P '      0               $' > /shahlab/tfunnell/bcbio_work/CX5461_yeast/work/varscan/chrVII/tx/tmp0mtxEk/tx/tmpquAJlC/SA779-chrVII_1084896_1090940-raw.mpileup\r\n[mpileup] 1 samples in 1 input files\r\n<mpileup> Set max per-file depth to 8000\r\n' returned non-zero exit status 1\r\n[2015-12-10T03:06Z] Genotyping with varscan: ('chrM', 0, 85779) 47_2015-12-05_CX5461_yeast-sort-chrM_0_85779-prep.bam\r\n[2015-12-10T03:06Z] mpileup for Varscan\r\nTraceback (most recent call last):\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/bin/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/bin/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 37, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 80, in _run_toplevel\r\n    for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 164, in run\r\n    samples = genotype.parallel_variantcall_region(samples, run_parallel)\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py\", line 167, in parallel_variantcall_region\r\n    \"vrn_file\", [\"region\", \"sam_ref\", \"config\"]))\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py\", line 32, in grouped_parallel_split_combine\r\n    final_output = parallel_fn(parallel_name, split_args)\r\nFile \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 28, in run_parallel\r\n    return run_multicore(fn, items, config, parallel=parallel)\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 86, in run_multicore\r\n    for data in joblib.Parallel(parallel[\"num_jobs\"])(joblib.delayed(fn)(x) for x in items):\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 664, in __call__\r\n    self.retrieve()\r\n  File \"/shahlab/tfunnell/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 547, in retrieve\r\n    raise exception_type(report)\r\nTypeError: __init__() takes at least 3 arguments (2 given)\r\nException in thread Thread-1 (most likely raised during interpreter shutdown):\r\n```\r\nRe-running the pipeline in serial mode results in the CalledProcessError above."}}