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anbrooks / juncBASE

Junction Based Analysis of Splicing Events for RNA-Seq
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Trying to compare different alternative splicing tools and running into some errors with juncBASE #13

Open asb3773 opened 3 years ago

asb3773 commented 3 years ago

I ran the following command: python juncBASE/run_preProcess_by_chr_step1.py -i bamInput.txt -o /stor/work/FRI-BigDataBio/alternativeSplicing/PSI-Sigma/cfolder --preProcess_options "–unique -c 1" -p 2

I am running into this error:

IOError: [Errno 24] Too many open files: '/stor/work/FRI-BigDataBio/alternativeSplicing/PSI-Sigma/cfolder/sample1/sample1_chrGL000226.1/sample1_chrGL000226.1_genome_reads.txt.gz' Traceback (most recent call last): File "/stor/work/FRI-BigDataBio/alternativeSplicing/juncBASE/juncBASE/preProcess_getASEventReadCounts_by_chr.py", line 904, in File "/stor/work/FRI-BigDataBio/alternativeSplicing/juncBASE/juncBASE/preProcess_getASEventReadCounts_by_chr.py", line 353, in main File "/usr/lib/python2.7/gzip.py", line 34, in open File "/usr/lib/python2.7/gzip.py", line 94, in init IOError: [Errno 24] Too many open files: '/stor/work/FRI-BigDataBio/alternativeSplicing/PSI-Sigma/cfolder/sample2/sample2_chrGL000226.1/sample2_chrGL000226.1_genome_reads.txt.gz'

Am I running something wrong? Where should I go from here?