{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1900","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1900/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1900/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1900/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1900","id":221726290,"number":1900,"title":"CalledProcessError of prepare_fish_for_sleuth()","user":{"login":"csardas","id":1390516,"avatar_url":"https://avatars2.githubusercontent.com/u/1390516?v=3","gravatar_id":"","url":"https://api.github.com/users/csardas","html_url":"https://github.com/csardas","followers_url":"https://api.github.com/users/csardas/followers","following_url":"https://api.github.com/users/csardas/following{/other_user}","gists_url":"https://api.github.com/users/csardas/gists{/gist_id}","starred_url":"https://api.github.com/users/csardas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/csardas/subscriptions","organizations_url":"https://api.github.com/users/csardas/orgs","repos_url":"https://api.github.com/users/csardas/repos","events_url":"https://api.github.com/users/csardas/events{/privacy}","received_events_url":"https://api.github.com/users/csardas/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2017-04-14T02:13:45Z","updated_at":"2017-04-20T01:16:36Z","closed_at":null,"body":"hi, \r\nI upgraded bcbio to 1.0.3a yesterday, RNAseq pipeline was broke in following processes:\r\n\r\n```\r\n  File \"/peterhouse/tools/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/salmon.py\", line 46, in run_salmon_reads\r\n    out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data)\r\n  File \"/peterhouse/tools/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/salmon.py\", line 84, in salmon_quant_reads\r\n    sailfish.sleuthify_sailfish(tx_out_dir)\r\n  File \"/peterhouse/tools/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/sailfish.py\", line 87, in sleuthify_sailfish\r\n    do.run(cmd.format(**locals()), \"Converting Sailfish to Sleuth format.\")\r\n  File \"/peterhouse/tools/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 22, in run\r\n    _do_run(cmd, checks, log_stdout, env=env)\r\n  File \"/peterhouse/tools/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 102, in _do_run\r\n    raise subprocess.CalledProcessError(exitcode, error_msg)\r\nsubprocess.CalledProcessError: Command 'set -o pipefail; /peterhouse/tools/bcbio/anaconda/bin/Rscript -e 'library(\"wasabi\"); prepare_fish_for_sleuth(c(\"/peterhouse/data/RNAseq/analysis/ana01/SLY-S9/work/bcbiotx/tmpy94CCd/quant\"))'\r\nLoading required package: methods\r\nError in setnames(quant, c(\"target_id\", \"length\", \"tpm\", \"est_counts\")) : \r\n  Can't assign 4 names to a 5 column data.table\r\nCalls: prepare_fish_for_sleuth -> sapply -> lapply -> FUN -> setnames\r\nExecution halted\r\n' returned non-zero exit status 1\r\n\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/295527485","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1900#issuecomment-295527485","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1900","id":295527485,"user":{"login":"roryk","id":414586,"avatar_url":"https://avatars1.githubusercontent.com/u/414586?v=3","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"created_at":"2017-04-20T01:16:35Z","updated_at":"2017-04-20T01:16:35Z","body":"Thanks I fixed the bioconda recipe to be 0.2."}}
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