OSError: [Errno 2] No such file or directory in juncBASE

I am new to python and I want to do Alternative splicing Discovery by juncBase but at the first step of the juncBase's Manual I have a error:

sabah@sabah-virtual-machine:~/juncBase/juncBASE_v0.6 $ python2.7 runCufflinks.py -i IlluminaHBM_2.0_samp2test_bam.txt --txt_ref UCSC.hg19.knownGene_w_gene_symbol_EnsemblChr.gtf --out_dir /home/sabah/juncBase/juncBASE_v0.6/out --num_processes 2
cufflinks -o /home/sabah/juncBase/juncBASE_v0.6/out/kidney_cufflinks -g UCSC.hg19.knownGene_w_gene_symbol_EnsemblChr.gtf -u kidney.bam
Traceback (most recent call last): File "runCufflinks.py", line 242, in <module> if __name__ == "__main__": main() File "runCufflinks.py", line 201, in main Popen(cmd, shell=True, executable=SHELL) File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception
OSError: [Errno 2] No such file or directory

Can you help me? When I typed python2.7 runCufflinks.py, the arguments of this command are shown.

1 Answer

Python can't find a file mentioned. Looking at the source code and manual, it mentions this:

You may need to modify this file [IlluminaHBM_2.0_samp2test_bam.txt] to specify the full path of the bam files

So in your case you may not have downloaded the test files or need to edit IlluminaHBM_2.0_samp2test_bam.txt to look something like this:

kidney /home/sabah/juncBase/juncBASE_v0.6/kidney.bam
breast /home/sabah/juncBase/juncBASE_v0.6/breast.bam
adrenal /home/sabah/juncBase/juncBASE_v0.6/adrenal.bam
colon /home/sabah/juncBase/juncBASE_v0.6/colon.bam
lung /home/sabah/juncBase/juncBASE_v0.6/lung.bam
liver /home/sabah/juncBase/juncBASE_v0.6/liver.bam