I am trying to analyze circular RNA. I have used STAR for alignment and DCC for detection. after this, I am trying to run FUCHS using the following parameters:
FUCHS -D /RNA/rna_anal/circrna/DCC/CircRNACount \
-J /RNA/rna_anal/circrna/sortedbam_paired/mkAChimeric.out.junction \
-F /RNA/rna_anal/circrna/sortedBam_mate1/mkA.1Chimeric.out.junction \
-R /RNA/rna_anal/circrna/sortedbam_mate2/mkA.2Chimeric.out.junction.fixed \
-B /RNA/rna_anal/circrna/mate1_2_mergedbam/mkA.merged.bam \
-A /RNA/rna_anal/circrna/bed.BED \
-r 2 \
-q 2 \
-p ensembl
-e 2 \
-T ~/tmp \
-P 7 \
-N mkA \
But I found the following error.
File "/home/mamu/.local/lib/python2.7/site-packages/FUCHS-0.2.0-py2.7.egg/FUCHS/FUCHS.py", line 179, in main
`output_file = open('%s/%s.logfile.%s' % (outfolder, sample, dt.replace(' ', '_')), 'w')`
IOError: [Errno 22] invalid mode ('w') or filename: '/RNA/rna_anal/circrna/FUCHS//mkA.logfile.2020-05-07_20:28:35.094516'
I have tried to find any solution on the FUCHS manual here and on google, unfortunately, I wasn't able to get any solution so far. Could you help me in solving this error, please? Thank you in advance for your help.
