Issue Encountered While Running FusionCatcher

[WANGW-z]

I am writing to report an issue I encountered while running FusionCatcher. During the process, I received the following error message:IOError: [Errno 2] No such file or directory: '/mnt/sdc/wwDatas/RGC_fusion/GSE236027_data/res/fusionca_res/SRR25052121/reads_ids_unmapped.txt'
fusioncatcher.log
info.txt
info.txt
fusioncatcher.log
@ndaniel @mpschr @yhoogstrate @wilcas @BSC-Support-Team

I would greatly appreciate it if you could help me resolve this issue!

[vinegang]

@WANGW-z I got the same error the other day. I am curious if you were able to fix it?

[WANGW-z]

Hi bro, @vinegang
After a series of debugging, I’ve finally resolved this issue. First of all, I’m not entirely sure whether the problem was caused by a version mismatch — here’s my current environment:
I'm using the above versions (including FusionCatcher 1.33 and Python 2.7.18), and I managed to fix the problem by modifying the file: /home/wangwen/Biosoft/ENTER/envs/fusioncatcher/bin/build_report_fusions_psl2.py
Specifically, I changed this original code block:
if options.input_unmapped_reads_filename: print "Reading...", options.input_unmapped_reads_filename unmapped_reads = set([line.rstrip('\r\n') for line in file(options.input_unmapped_reads_filename,'r').readlines()])
👉 ​​To this safer version with exception handling:​
if options.input_unmapped_reads_filename: print "Reading...", options.input_unmapped_reads_filename try: unmapped_reads = set([line.rstrip('\r\n') for line in open(options.input_unmapped_reads_filename, 'r')]) except IOError: print "Warning: Unmapped reads file '%s' not found. Skipping." % options.input_unmapped_reads_filename unmapped_reads = set()

🎉 ​​After this change, the script no longer throws an error when the reads_ids_unmapped.txtfile is missing, and the entire process runs smoothly without crashing.​