{"action":"opened","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/973","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/973/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/973/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/973/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/973","id":100661373,"number":973,"title":"dexseq_count.py issue in a RNAseq run","user":{"login":"scatreux","id":6052383,"avatar_url":"https://avatars.githubusercontent.com/u/6052383?v=3","gravatar_id":"","url":"https://api.github.com/users/scatreux","html_url":"https://github.com/scatreux","followers_url":"https://api.github.com/users/scatreux/followers","following_url":"https://api.github.com/users/scatreux/following{/other_user}","gists_url":"https://api.github.com/users/scatreux/gists{/gist_id}","starred_url":"https://api.github.com/users/scatreux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/scatreux/subscriptions","organizations_url":"https://api.github.com/users/scatreux/orgs","repos_url":"https://api.github.com/users/scatreux/repos","events_url":"https://api.github.com/users/scatreux/events{/privacy}","received_events_url":"https://api.github.com/users/scatreux/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-08-12T23:59:12Z","updated_at":"2015-08-12T23:59:12Z","closed_at":null,"body":"Hi\r\n\r\nI'm hitting an issue consistently on a RNASeq run.\r\nBelow is the error:\r\n\r\n[2015-08-12T23:53Z] multiprocessing: run_cufflinks\r\n[2015-08-12T23:53Z] Resource requests: dexseq, express; memory: 1.00; cores: 1, 1\r\n[2015-08-12T23:53Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2015-08-12T23:53Z] Timing: estimate expression (single threaded)\r\n[2015-08-12T23:53Z] multiprocessing: run_express\r\n[2015-08-12T23:53Z] Transcriptome-mapped BAM file not found, skipping eXpress.\r\n[2015-08-12T23:53Z] multiprocessing: run_dexseq\r\n[2015-08-12T23:53Z] Counting exon-level counts with /staging/edico_s/results/seqc_SRR950078_15M/work/align/UHRR_rep1/1_2015-03-10_seqc_star/UHRR_rep1.bam and /mnt/vault/reference_genomes/Hsapiens/GRCh37/rnaseq/../rnaseq/ref-transcripts.dexseq.gff.\r\n[2015-08-12T23:54Z] Traceback (most recent call last):\r\n[2015-08-12T23:54Z]   File \"/usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py\", line 239, in <module>\r\n[2015-08-12T23:54Z]     if current_chromosome != a.iv.chrom:\r\n[2015-08-12T23:54Z] AttributeError: 'NoneType' object has no attribute 'chrom'\r\n[2015-08-12T23:54Z] Uncaught exception occurred\r\nTraceback (most recent call last):\r\n  File \"/usr/local/share/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 \"/usr/local/share/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; /usr/local/share/bcbio-nextgen/anaconda/bin/python /usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py -f bam -r pos -p yes -s no /mnt/vault/reference_genomes/Hsapiens/GRCh37/rnaseq/../rnaseq/ref-transcripts.dexseq.gff /staging/edico_s/results/seqc_SRR950078_15M/work/align/UHRR_rep1/1_2015-03-10_seqc_star/UHRR_rep1.bam /staging/edico_s/results/seqc_SRR950078_15M/work/dexseq/tx/tmpbXBA0u/UHRR_rep1.dexseq\r\nTraceback (most recent call last):\r\n  File \"/usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py\", line 239, in <module>\r\n    if current_chromosome != a.iv.chrom:\r\nAttributeError: 'NoneType' object has no attribute 'chrom'\r\n' returned non-zero exit status 1\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/usr/local/bin/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/usr/local/share/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 \"/usr/local/share/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 \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 311, in run\r\n    samples = rnaseq.quantitate_expression_noparallel(samples, run_parallel)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py\", line 53, in quantitate_expression_noparallel\r\n    samples = run_parallel(\"run_dexseq\", samples)\r\n  File \"/usr/local/share/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 \"/usr/local/share/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 \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 657, in __call__\r\n    self.dispatch(function, args, kwargs)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 404, in dispatch\r\n    job = ImmediateApply(func, args, kwargs)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 142, in __init__\r\n    self.results = func(*args, **kwargs)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 49, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 118, in run_dexseq\r\n    return rnaseq.run_dexseq(*args)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py\", line 93, in run_dexseq\r\n    data = dexseq.bcbio_run(data)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/dexseq.py\", line 23, in bcbio_run\r\n    counts = run_count(bam_file, dexseq_gff, stranded, out_file, data)\r\n  File \"/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/dexseq.py\", line 64, in run_count\r\n    do.run(cmd.format(**locals()), message)\r\n  File \"/usr/local/share/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 \"/usr/local/share/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\nsubprocess.CalledProcessError: Command 'set -o pipefail; /usr/local/share/bcbio-nextgen/anaconda/bin/python /usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py -f bam -r pos -p yes -s no /mnt/vault/reference_genomes/Hsapiens/GRCh37/rnaseq/../rnaseq/ref-transcripts.dexseq.gff /staging/edico_s/results/seqc_SRR950078_15M/work/align/UHRR_rep1/1_2015-03-10_seqc_star/UHRR_rep1.bam /staging/edico_s/results/seqc_SRR950078_15M/work/dexseq/tx/tmpbXBA0u/UHRR_rep1.dexseq\r\nTraceback (most recent call last):\r\n  File \"/usr/local/lib/R/site-library/DEXSeq/python_scripts/dexseq_count.py\", line 239, in <module>\r\n    if current_chromosome != a.iv.chrom:\r\nAttributeError: 'NoneType' object has no attribute 'chrom'\r\n' returned non-zero exit status 1\r\n"}}