{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1402","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1402/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1402/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1402/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1402","id":156419634,"number":1402,"title":"small rna seq (multiqc error)","user":{"login":"hmkim","id":4966343,"avatar_url":"https://avatars.githubusercontent.com/u/4966343?v=3","gravatar_id":"","url":"https://api.github.com/users/hmkim","html_url":"https://github.com/hmkim","followers_url":"https://api.github.com/users/hmkim/followers","following_url":"https://api.github.com/users/hmkim/following{/other_user}","gists_url":"https://api.github.com/users/hmkim/gists{/gist_id}","starred_url":"https://api.github.com/users/hmkim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hmkim/subscriptions","organizations_url":"https://api.github.com/users/hmkim/orgs","repos_url":"https://api.github.com/users/hmkim/repos","events_url":"https://api.github.com/users/hmkim/events{/privacy}","received_events_url":"https://api.github.com/users/hmkim/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-24T04:54:18Z","updated_at":"2016-05-24T07:24:24Z","closed_at":null,"body":"> [2016-05-24T04:37Z] summarize variants\r\n> [2016-05-24T04:37Z] Run multiqc\r\n> [2016-05-24T04:37Z] [INFO   ]         multiqc : This is MultiQC v0.6\r\n> [2016-05-24T04:37Z] [INFO   ]         multiqc : Searching 'trimmed'\r\n> [2016-05-24T04:37Z] [WARNING]         multiqc : No analysis results found. Cleaning up..\r\n> [2016-05-24T04:37Z] [INFO   ]         multiqc : MultiQC complete\r\n> Traceback (most recent call last):\r\n>   File \"/BiO/BioTools/bcbio/tools/bin/bcbio_nextgen.py\", line 226, in <module>\r\n>     main(**kwargs)\r\n>   File \"/BiO/BioTools/bcbio/tools/bin/bcbio_nextgen.py\", line 43, in main\r\n>     run_main(**kwargs)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 43, in run_main\r\n>     fc_dir, run_info_yaml)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 87, in _run_toplevel\r\n>     for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 328, in smallrnaseqpipeline\r\n>     samples = qcsummary.generate_parallel(samples, run_parallel)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 26, in generate_parallel\r\n>     samples = run_parallel(\"multiqc_summary\", [samples])\r\n>   File \"/BiO/BioTools/bcbio/data/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 \"/BiO/BioTools/bcbio/data/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 \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n>     while self.dispatch_one_batch(iterator):\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n>     self._dispatch(tasks)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n>     job = ImmediateComputeBatch(batch)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n>     self.results = batch()\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 72, in __call__\r\n>     return [func(*args, **kwargs) for func, args, kwargs in self.items]\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n>     return apply(f, *args, **kwargs)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 140, in multiqc_summary\r\n>     return multiqc.summary(*args)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/qc/multiqc.py\", line 51, in summary\r\n>     shutil.move(os.path.join(tx_out, \"multiqc_report.html\"), out_file)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/shutil.py\", line 302, in move\r\n>     copy2(src, real_dst)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/shutil.py\", line 130, in copy2\r\n>     copyfile(src, dst)\r\n>   File \"/BiO/BioTools/bcbio/data/anaconda/lib/python2.7/shutil.py\", line 82, in copyfile\r\n>     with open(src, 'rb') as fsrc:\r\n> IOError: [Errno 2] No such file or directory: '/BiO/BioProjects/Project/Project-merged/work/tx/tmpvM20wC/multiqc_report.html'\r\n\r\nCan you check this error in small rna seq workflow?\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/221187278","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1402#issuecomment-221187278","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1402","id":221187278,"user":{"login":"hmkim","id":4966343,"avatar_url":"https://avatars.githubusercontent.com/u/4966343?v=3","gravatar_id":"","url":"https://api.github.com/users/hmkim","html_url":"https://github.com/hmkim","followers_url":"https://api.github.com/users/hmkim/followers","following_url":"https://api.github.com/users/hmkim/following{/other_user}","gists_url":"https://api.github.com/users/hmkim/gists{/gist_id}","starred_url":"https://api.github.com/users/hmkim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hmkim/subscriptions","organizations_url":"https://api.github.com/users/hmkim/orgs","repos_url":"https://api.github.com/users/hmkim/repos","events_url":"https://api.github.com/users/hmkim/events{/privacy}","received_events_url":"https://api.github.com/users/hmkim/received_events","type":"User","site_admin":false},"created_at":"2016-05-24T07:24:24Z","updated_at":"2016-05-24T07:24:24Z","body":"```\r\n 42     # Back compatible -- to migrate to explicit specifications in input YAML\r\n 43     folders += [\"trimmed\", \"htseq-count/*summary\"]\r\n 44     if not utils.file_exists(out_file):\r\n 45         with utils.chdir(work_dir):\r\n 46             input_dir = \" \".join([_check_multiqc_input(d) for d in folders])\r\n 47             if input_dir.strip():\r\n 48                 cmd = \"{multiqc} -f {input_dir} -o {tx_out} {opts}\"\r\n 49                 with tx_tmpdir(data, work_dir) as tx_out:\r\n 50                     do.run(cmd.format(**locals()), \"Run multiqc\")\r\n 51                     shutil.move(os.path.join(tx_out, \"multiqc_report.html\"), out_file)\r\n 52                     shutil.move(os.path.join(tx_out, \"multiqc_data\"), out_data)\r\n 53     out = []\r\n```\r\nWhen I block the line of 51, 52, I finished job.\r\n\r\nWhy don't have the result of multiqc? Anyway, in case of this need the passing of this step."}}
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