GitHub PushEvent at 2014-05-05 17:39:31
Repository: pipeline
Actor: semenko
Payload: {"shas":[["df680cc55c846acc4a914f6581e550f91101b887","a942b7ac730822f3cc660013817af0e530d155cc@gmail.com","allow gene mapping to run w/o bam and default call gene mapping on all super/stretch output in ROSE2_main","Charles Lin",true],["6f42f7023788c0c186157d8f30563ce1e4ed5123","ea6933c840f4d406403426b60ebb5f2e03981b9c@alum.mit.edu","Fixes output directory error, I think.\n\nMAKING TSS COLLECTION\nMAKING ENHANCER ASSOCIATED GENE TSS COLLECTION\nMAPPING SIGNAL AT ENHANCER ASSOCIATED GENE TSS\nMapping rankby bam ../sshfs/4_dedupe/CONV4_CD4.nomito.rmdup.bam\npython bamliquidator_batch.py --sense . -e 200 --match_bamToGFF -r ../sshfs/x_rose/CONV4_CD4/mm9_TSS_ENHANCER_GENES_-5000_+5000.gff -o ../sshfs/x_rose/CONV4_CD4/mm9_TSS_ENHANCER_GENES_-5000_+5000_CONV4_CD4.nomito.rmdup.bam/ ../sshfs/4_dedupe/CONV4_CD4.nomito.rmdup.bam\nTraceback (most recent call last):\n  File \"bamliquidator_batch.py\", line 343, in <module>\n    main()\n  File \"bamliquidator_batch.py\", line 326, in main\n    liquidator = RegionLiquidator(args.regions_file, args.output_directory, args.bam_file_path, args.counts_file)\n  File \"bamliquidator_batch.py\", line 214, in __init__\n    super(RegionLiquidator, self).__init__(\"bamliquidator_regions\", \"region_counts\", output_directory, bam_file_path, counts_file_path)\n  File \"bamliquidator_batch.py\", line 104, in __init__\n    os.mkdir(output_directory)\nOSError: [Errno 17] File exists: '../sshfs/x_rose/CONV4_CD4/mm9_TSS_ENHANCER_GENES_-5000_+5000_CONV4_CD4.nomito.rmdup.bam/'\nERROR: FAILED TO MAP ../sshfs/x_rose/CONV4_CD4/mm9_TSS_ENHANCER_GENES_-5000_+5000.gff FROM BAM: ../sshfs/4_dedupe/CONV4_CD4.nomito.rmdup.bam\n{'control': '', 'geneList': None, 'rankby': '../sshfs/4_dedupe/CONV4_CD4.nomito.rmdup.bam', 'window': 50000, 'genome': 'mm9', 'input': '../sshfs/x_rose/CONV4_CD4/CONV4_CD4_SuperStretchEnhancers.table.txt', 'formatTable': False, 'out': None}\nUSING mm9 AS THE GENOME\nMAKING TRANSCRIPT COLLECTION","Nick Semenkovich",true]],"size":2,"ref":"refs/heads/rose2-cleanups","head":"6f42f7023788c0c186157d8f30563ce1e4ed5123"}