BradnerLab/pipeline — pull request #8 by semenko (2014-05-05 17:40:01+00:00)
Title: Fixes output directory error, I think.

MAKING TSS COLLECTION
MAKING ENHANCER ASSOCIATED GENE TSS COLLECTION
MAPPING SIGNAL AT ENHANCER ASSOCIATED GENE TSS
Mapping rankby bam ../sshfs/4_dedupe/CONV4_CD4.nomito.rmdup.bam
python 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
Traceback (most recent call last):
File "bamliquidator_batch.py", line 343, in
main()
File "bamliquidator_batch.py", line 326, in main
liquidator = RegionLiquidator(args.regions_file, args.output_directory, args.bam_file_path, args.counts_file)
File "bamliquidator_batch.py", line 214, in __init__
super(RegionLiquidator, self).__init__("bamliquidator_regions", "region_counts", output_directory, bam_file_path, counts_file_path)
File "bamliquidator_batch.py", line 104, in __init__
os.mkdir(output_directory)
OSError: [Errno 17] File exists: '../sshfs/x_rose/CONV4_CD4/mm9_TSS_ENHANCER_GENES_-5000_+5000_CONV4_CD4.nomito.rmdup.bam/'
ERROR: 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
{'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}
USING mm9 AS THE GENOME
MAKING TRANSCRIPT COLLECTION