{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1572","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1572/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1572/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1572/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1572","id":178884004,"number":1572,"title":"Test run error","user":{"login":"firatuyulur","id":20151383,"avatar_url":"https://avatars.githubusercontent.com/u/20151383?v=3","gravatar_id":"","url":"https://api.github.com/users/firatuyulur","html_url":"https://github.com/firatuyulur","followers_url":"https://api.github.com/users/firatuyulur/followers","following_url":"https://api.github.com/users/firatuyulur/following{/other_user}","gists_url":"https://api.github.com/users/firatuyulur/gists{/gist_id}","starred_url":"https://api.github.com/users/firatuyulur/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/firatuyulur/subscriptions","organizations_url":"https://api.github.com/users/firatuyulur/orgs","repos_url":"https://api.github.com/users/firatuyulur/repos","events_url":"https://api.github.com/users/firatuyulur/events{/privacy}","received_events_url":"https://api.github.com/users/firatuyulur/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-23T13:55:04Z","updated_at":"2016-09-23T14:11:31Z","closed_at":null,"body":"Hi,\r\nIts me again. I am using Bcbio on a new cluster. after installation I tried to run the test runs. especially rnaseq. I am having the error which I will post downstream. when I asked our university IT team about the error, they are thinking of a more fundamental error about file systems that terminologically I cannot rephrase very well. here is the error \r\n```\r\n[fiuyulur@yunus tests]$ ./run_tests.sh rnaseq\r\nRun a fast RNA-seq analysis ... [2016-09-23T13:46Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:46Z] Resource requests: picard; memory: 3.00; cores: 16\r\n[2016-09-23T13:46Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:46Z] Timing: organize samples\r\n[2016-09-23T13:46Z] multiprocessing: organize_samples\r\n[2016-09-23T13:46Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-fastrnaseq.yaml\r\n[2016-09-23T13:46Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-fastrnaseq.yaml\r\n[2016-09-23T13:46Z] Testing minimum versions of installed programs\r\n[2016-09-23T13:46Z] multiprocessing: prepare_sample\r\n[2016-09-23T13:46Z] Preparing Test1\r\n[2016-09-23T13:46Z] Resource requests: samtools; memory: 3.00; cores: 16\r\n[2016-09-23T13:46Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:46Z] Timing: fastrnaseq\r\n[2016-09-23T13:46Z] multiprocessing: run_salmon_reads\r\n[2016-09-23T13:46Z] Extracting genomic sequences of /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf.\r\n[2016-09-23T13:46Z] Reading the annotation file: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf\r\n[2016-09-23T13:46Z] Creating Salmon index for /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/salmon/Test1/index/mm9/mm9.fa.\r\n[2016-09-23T13:46Z] Version Info: This is the most recent version of Salmon.\r\n[2016-09-23T13:46Z] index [\"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/salmon/Test1/index/tx/tmpeD6NZt/mm9\"] did not previously exist  . . . creating it\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:29.757] [jLog] [info] building index\r\n[2016-09-23T13:46Z] RapMap Indexer\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] [Step 1 of 4] : counting k-mers\r\n[2016-09-23T13:46Z] Elapsed time: 0.008873s\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] Replaced 0 non-ATCG nucleotides\r\n[2016-09-23T13:46Z] Clipped poly-A tails from 0 transcripts\r\n[2016-09-23T13:46Z] Building rank-select dictionary and saving to disk done\r\n[2016-09-23T13:46Z] Elapsed time: 0.001397s\r\n[2016-09-23T13:46Z] Writing sequence data to file . . . done\r\n[2016-09-23T13:46Z] Elapsed time: 0.000958s\r\n[2016-09-23T13:46Z] [info] Building 32-bit suffix array (length of generalized text is 15574)\r\n[2016-09-23T13:46Z] Building suffix array . . . success\r\n[2016-09-23T13:46Z] saving to disk . . . done\r\n[2016-09-23T13:46Z] Elapsed time: 0.002701s\r\n[2016-09-23T13:46Z] done\r\n[2016-09-23T13:46Z] Elapsed time: 0.029378s\r\nprocessed 0 positions\r\n[2016-09-23T13:46Z] khash had 14382 keys\r\n[2016-09-23T13:46Z] saving hash to disk . . . done\r\n[2016-09-23T13:46Z] Elapsed time: 0.003464s\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:29.858] [jLog] [info] done building index\r\n[2016-09-23T13:46Z] Quantifying transcripts in /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz and /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz with Salmon.\r\n[2016-09-23T13:46Z] Version Info: This is the most recent version of Salmon.\r\n[2016-09-23T13:46Z] ### salmon (mapping-based) v0.7.2\r\n[2016-09-23T13:46Z] ### [ program ] => salmon\r\n[2016-09-23T13:46Z] ### [ command ] => quant\r\n[2016-09-23T13:46Z] ### [ libType ] => { IU }\r\n[2016-09-23T13:46Z] ### [ index ] => { /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/salmon/Test1/index/mm9 }\r\n[2016-09-23T13:46Z] ### [ threads ] => { 1 }\r\n[2016-09-23T13:46Z] ### [ output ] => { /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/salmon/Test1/tx/tmpk5N06T/quant }\r\n[2016-09-23T13:46Z] ### [ mates1 ] => { /dev/fd/63 }\r\n[2016-09-23T13:46Z] ### [ mates2 ] => { /dev/fd/62 }\r\n[2016-09-23T13:46Z] ### [ numBootstraps ] => { 30 }\r\n[2016-09-23T13:46Z] Logs will be written to /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/salmon/Test1/tx/tmpk5N06T/quant/logs\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.608] [jointLog] [info] parsing read library format\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.609] [jointLog] [info] There is 1 library.\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.815] [jointLog] [info] Loading Quasi index\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.816] [jointLog] [info] Loading 32-bit quasi index\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.822] [jointLog] [info] done\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.823] [jointLog] [info] Index contained 38 targets\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.817] [stderrLog] [info] Loading Suffix Array\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.820] [stderrLog] [info] Loading Transcript Info\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.820] [stderrLog] [info] Successfully loaded position hash\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.821] [stderrLog] [info] Loading Rank-Select Bit Array\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.822] [stderrLog] [info] There were 38 set bits in the bit array\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.822] [stderrLog] [info] Computing transcript lengths\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.822] [stderrLog] [info] Waiting to finish loading hash\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:30.822] [stderrLog] [info] Done loading index\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.937] [jointLog] [info] Computed 3 rich equivalence classes for further processing\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.937] [jointLog] [info] Counted 18956 total reads in the equivalence classes\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.940] [jointLog] [warning] Only 18956 fragments were mapped, but the number of burn-in fragments was set to 5000000.\r\n[2016-09-23T13:46Z] The effective lengths have been computed using the observed mappings.\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.940] [jointLog] [info] Mapping rate = 75.824%\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.940] [jointLog] [info] finished quantifyLibrary()\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.942] [jointLog] [info] Starting optimizer\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.952] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.952] [jointLog] [info] iteration = 0 | max rel diff. = 497.9\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.952] [jointLog] [info] iteration = 100 | max rel diff. = 0\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.952] [jointLog] [info] Finished optimizer\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.952] [jointLog] [info] writing output\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.968] [jointLog] [info] Starting Bootstrapping\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.968] [jointLog] [info] Will draw 30 bootstrap samples\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.968] [jointLog] [info] Optimizing over 3 equivalence classes\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.968] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.970] [jointLog] [info] wrote 1 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.971] [jointLog] [info] wrote 2 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.972] [jointLog] [info] wrote 3 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.972] [jointLog] [info] wrote 4 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.973] [jointLog] [info] wrote 5 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.974] [jointLog] [info] wrote 6 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.974] [jointLog] [info] wrote 7 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.975] [jointLog] [info] wrote 8 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.976] [jointLog] [info] wrote 9 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.976] [jointLog] [info] wrote 10 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.977] [jointLog] [info] wrote 11 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.977] [jointLog] [info] wrote 12 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.978] [jointLog] [info] wrote 13 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.979] [jointLog] [info] wrote 14 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.979] [jointLog] [info] wrote 15 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.980] [jointLog] [info] wrote 16 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.981] [jointLog] [info] wrote 17 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.981] [jointLog] [info] wrote 18 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.982] [jointLog] [info] wrote 19 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.983] [jointLog] [info] wrote 20 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.983] [jointLog] [info] wrote 21 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.984] [jointLog] [info] wrote 22 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.984] [jointLog] [info] wrote 23 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.985] [jointLog] [info] wrote 24 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.986] [jointLog] [info] wrote 25 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.986] [jointLog] [info] wrote 26 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.987] [jointLog] [info] wrote 27 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.988] [jointLog] [info] wrote 28 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.988] [jointLog] [info] wrote 29 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.989] [jointLog] [info] wrote 30 bootstraps\r\n[2016-09-23T13:46Z] [2016-09-23 16:46:31.989] [jointLog] [info] Finished Bootstrapping\r\n[2016-09-23T13:46Z] \r\n[2016-09-23T13:46Z] Combining count files into /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/sailfish/combined.sf.\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 280, in fastrnaseqpipeline\r\n    samples = rnaseq.fast_rnaseq(samples, run_parallel)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py\", line 14, in fast_rnaseq\r\n    samples = sailfish.combine_sailfish(samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/sailfish.py\", line 195, in combine_sailfish\r\n    tdf = pd.DataFrame.from_dict(gtf.transcript_to_gene(gtf_file),\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 293, in transcript_to_gene\r\n    for feature in complete_features(get_gtf_db(gtf)):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 42, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 130, in __init__\r\n    ''')\r\nsqlite3.OperationalError: disk I/O error\r\nERROR\r\nRun an RNA-seq analysis with hisat2 and generate gene-level counts. ... [2016-09-23T13:46Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:46Z] Resource requests: cutadapt, picard; memory: 3.00, 3.00; cores: 16, 16\r\n[2016-09-23T13:46Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:46Z] Timing: organize samples\r\n[2016-09-23T13:46Z] multiprocessing: organize_samples\r\n[2016-09-23T13:46Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-hisat2.yaml\r\n[2016-09-23T13:46Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-hisat2.yaml\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 237, in rnaseqpipeline\r\n    samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 389, in rnaseq_prep_samples\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n    self.results = batch()\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 300, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 67, in organize\r\n    item[\"config\"][\"algorithm\"][\"qc\"] = qcsummary.get_qc_tools(item)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 74, in get_qc_tools\r\n    if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 306, in is_qualimap_compatible\r\n    db = get_gtf_db(gtf)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 42, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 130, in __init__\r\n    ''')\r\nsqlite3.OperationalError: disk I/O error\r\nERROR\r\nRun an RNA-seq analysis with TopHat and generate gene-level counts. ... [2016-09-23T13:47Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:47Z] Resource requests: cutadapt, picard; memory: 3.00, 3.00; cores: 16, 16\r\n[2016-09-23T13:47Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:47Z] Timing: organize samples\r\n[2016-09-23T13:47Z] multiprocessing: organize_samples\r\n[2016-09-23T13:47Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-rnaseq.yaml\r\n[2016-09-23T13:47Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-rnaseq.yaml\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 237, in rnaseqpipeline\r\n    samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 389, in rnaseq_prep_samples\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n    self.results = batch()\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 300, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 67, in organize\r\n    item[\"config\"][\"algorithm\"][\"qc\"] = qcsummary.get_qc_tools(item)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 74, in get_qc_tools\r\n    if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 306, in is_qualimap_compatible\r\n    db = get_gtf_db(gtf)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 42, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 130, in __init__\r\n    ''')\r\nsqlite3.OperationalError: disk I/O error\r\nERROR\r\nRun a single-cell RNA-seq analysis ... [2016-09-23T13:47Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:47Z] Resource requests: picard; memory: 3.00; cores: 16\r\n[2016-09-23T13:47Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:47Z] Timing: organize samples\r\n[2016-09-23T13:47Z] multiprocessing: organize_samples\r\n[2016-09-23T13:47Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-scrnaseq.yaml\r\n[2016-09-23T13:47Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-scrnaseq.yaml\r\n[2016-09-23T13:47Z] Testing minimum versions of installed programs\r\n[2016-09-23T13:47Z] multiprocessing: prepare_sample\r\n[2016-09-23T13:47Z] Preparing Test1\r\n[2016-09-23T13:47Z] Resource requests: samtools; memory: 3.00; cores: 16\r\n[2016-09-23T13:47Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:47Z] Timing: singlecell-rnaseq\r\n[2016-09-23T13:47Z] multiprocessing: run_umi_transform\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 295, in singlecellrnaseqpipeline\r\n    samples = rnaseq.singlecell_rnaseq(samples, run_parallel)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py\", line 21, in singlecell_rnaseq\r\n    samples = run_parallel(\"run_umi_transform\", samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n    self.results = batch()\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 32, in run_umi_transform\r\n    return umi.umi_transform(*args)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/umi.py\", line 80, in umi_transform\r\n    umis = config_utils.get_program(\"umis\", data, default=\"umis\")\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py\", line 186, in get_program\r\n    return _get_program_cmd(name, pconfig, config, default)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py\", line 212, in wrap\r\n    raise CmdNotFound(\" \".join(map(repr, (fn.func_name, name, pconfig, default))))\r\nbcbio.pipeline.config_utils.CmdNotFound: '_get_program_cmd' 'umis' {} 'umis'\r\nSKIP\r\nRun an RNA-seq analysis with STAR and generate gene-level counts. ... [2016-09-23T13:47Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:47Z] Resource requests: cutadapt, picard; memory: 3.00, 3.00; cores: 16, 16\r\n[2016-09-23T13:47Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:47Z] Timing: organize samples\r\n[2016-09-23T13:47Z] multiprocessing: organize_samples\r\n[2016-09-23T13:47Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-star.yaml\r\n[2016-09-23T13:47Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-star.yaml\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 237, in rnaseqpipeline\r\n    samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 389, in rnaseq_prep_samples\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n    self.results = batch()\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 300, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 67, in organize\r\n    item[\"config\"][\"algorithm\"][\"qc\"] = qcsummary.get_qc_tools(item)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 74, in get_qc_tools\r\n    if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 306, in is_qualimap_compatible\r\n    db = get_gtf_db(gtf)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 42, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 130, in __init__\r\n    ''')\r\nsqlite3.OperationalError: disk I/O error\r\nERROR\r\nRun an RNA-seq analysis with TopHat and generate gene-level counts. ... [2016-09-23T13:48Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:48Z] Resource requests: cutadapt, picard; memory: 3.00, 3.00; cores: 16, 16\r\n[2016-09-23T13:48Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:48Z] Timing: organize samples\r\n[2016-09-23T13:48Z] multiprocessing: organize_samples\r\n[2016-09-23T13:48Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-stranded.yaml\r\n[2016-09-23T13:48Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-stranded.yaml\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 237, in rnaseqpipeline\r\n    samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 389, in rnaseq_prep_samples\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n    self.results = batch()\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 300, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 67, in organize\r\n    item[\"config\"][\"algorithm\"][\"qc\"] = qcsummary.get_qc_tools(item)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 74, in get_qc_tools\r\n    if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 306, in is_qualimap_compatible\r\n    db = get_gtf_db(gtf)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 42, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 130, in __init__\r\n    ''')\r\nsqlite3.OperationalError: disk I/O error\r\nERROR\r\nRun an explant RNA-seq analysis with TopHat and generate gene-level counts. ... [2016-09-23T13:48Z] System YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml\r\n/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/psutil/_pslinux.py:338: RuntimeWarning: shared memory stats couldn't be determined and was set to 0\r\n  warnings.warn(msg, RuntimeWarning)\r\n[2016-09-23T13:48Z] Resource requests: cutadapt, picard; memory: 3.00, 3.00; cores: 16, 16\r\n[2016-09-23T13:48Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job\r\n[2016-09-23T13:48Z] Timing: organize samples\r\n[2016-09-23T13:48Z] multiprocessing: organize_samples\r\n[2016-09-23T13:48Z] Using input YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-explant.yaml\r\n[2016-09-23T13:48Z] Checking sample YAML configuration: /mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-explant.yaml\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py\", line 1484, in run_script\r\n    \r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 237, in rnaseqpipeline\r\n    samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 389, in rnaseq_prep_samples\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 800, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 658, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 566, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 180, in __init__\r\n    self.results = batch()\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/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 \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 51, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 300, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 67, in organize\r\n    item[\"config\"][\"algorithm\"][\"qc\"] = qcsummary.get_qc_tools(item)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/qcsummary.py\", line 74, in get_qc_tools\r\n    if gtf.is_qualimap_compatible(dd.get_gtf_file(data)):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 306, in is_qualimap_compatible\r\n    db = get_gtf_db(gtf)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 42, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 130, in __init__\r\n    ''')\r\nsqlite3.OperationalError: disk I/O error\r\nERROR\r\n\r\n======================================================================\r\nERROR: Run a fast RNA-seq analysis\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_analysis.py\", line 206, in test_2_fastrnaseq\r\n    subprocess.check_call(cl)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/subprocess.py\", line 541, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-fastrnaseq.yaml']' returned non-zero exit status 1\r\n\r\n======================================================================\r\nERROR: Run an RNA-seq analysis with hisat2 and generate gene-level counts.\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_analysis.py\", line 235, in test_2_hisat2\r\n    subprocess.check_call(cl)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/subprocess.py\", line 541, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-hisat2.yaml']' returned non-zero exit status 1\r\n\r\n======================================================================\r\nERROR: Run an RNA-seq analysis with TopHat and generate gene-level counts.\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_analysis.py\", line 167, in test_2_rnaseq\r\n    subprocess.check_call(cl)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/subprocess.py\", line 541, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-rnaseq.yaml']' returned non-zero exit status 1\r\n\r\n======================================================================\r\nERROR: Run an RNA-seq analysis with STAR and generate gene-level counts.\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_analysis.py\", line 193, in test_2_star\r\n    subprocess.check_call(cl)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/subprocess.py\", line 541, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-star.yaml']' returned non-zero exit status 1\r\n\r\n======================================================================\r\nERROR: Run an RNA-seq analysis with TopHat and generate gene-level counts.\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_analysis.py\", line 154, in test_2_stranded\r\n    subprocess.check_call(cl)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/subprocess.py\", line 541, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/../test_stranded', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-stranded.yaml']' returned non-zero exit status 1\r\n\r\n======================================================================\r\nERROR: Run an explant RNA-seq analysis with TopHat and generate gene-level counts.\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_analysis.py\", line 250, in test_explant\r\n    subprocess.check_call(cl)\r\n  File \"/mnt/kufs/scratch/fiuyulur/bcbio_ku/share/bcbio/anaconda/lib/python2.7/subprocess.py\", line 541, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/../1_explant', '/mnt/kufs/scratch/fiuyulur/bcbio-nextgen/tests/data/automated/run_info-explant.yaml']' returned non-zero exit status 1\r\n\r\n----------------------------------------------------------------------\r\nRan 7 tests in 143.915s\r\n\r\nFAILED (SKIP=1, errors=6)```\r\n\r\nWhat do you think is happenning? Thanks already\r\nFırat"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/249203574","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1572#issuecomment-249203574","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1572","id":249203574,"user":{"login":"firatuyulur","id":20151383,"avatar_url":"https://avatars.githubusercontent.com/u/20151383?v=3","gravatar_id":"","url":"https://api.github.com/users/firatuyulur","html_url":"https://github.com/firatuyulur","followers_url":"https://api.github.com/users/firatuyulur/followers","following_url":"https://api.github.com/users/firatuyulur/following{/other_user}","gists_url":"https://api.github.com/users/firatuyulur/gists{/gist_id}","starred_url":"https://api.github.com/users/firatuyulur/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/firatuyulur/subscriptions","organizations_url":"https://api.github.com/users/firatuyulur/orgs","repos_url":"https://api.github.com/users/firatuyulur/repos","events_url":"https://api.github.com/users/firatuyulur/events{/privacy}","received_events_url":"https://api.github.com/users/firatuyulur/received_events","type":"User","site_admin":false},"created_at":"2016-09-23T14:11:31Z","updated_at":"2016-09-23T14:11:31Z","body":"Thanks for the quick reply Rory, I passed your answer to out IT team. I hope we will manage to fix it."}}
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