Traceback (most recent call last):
File "miniconda3/envs/irep-env/bin/iRep", line 73, in <module>
thresholds, args['no_gc_correction'], args['t'])
File "miniconda3/envs/irep-env/lib/python3.6/site-packages/iRep/iRep.py", line 976, in iRep
genomes, id2g = parse_genomes_fa(fastas, mappings)
File "miniconda3/envs/irep-env/lib/python3.6/site-packages/iRep/iRep.py", line 917, in parse_genomes_fa
ID = seq[0].split('>', 1)[1].split()[0]
AttributeError: 'list' object has no attribute 'split'
I process ~300 genomes in total, and tried running for ~950 samples (the test run hadn't crashed after some time, so I confidently submitted all jobs...). All of them crash, none provide output. Is something wrong with my input genomes? I indexed the samfiles, so I assume it's not about a weird stream sent by samtools.
I am running
iRep
on a large dataset, using the piping approach suggested by @nigiord in #1 , like so:My version is the latest one downloaded from bioconda, I assume 1.1.7 (not sure how to get the actual version number from the tool though...).
When running, I first get a warning (no clue if that's relevant):
The program then crashes with this error:
I process ~300 genomes in total, and tried running for ~950 samples (the test run hadn't crashed after some time, so I confidently submitted all jobs...). All of them crash, none provide output. Is something wrong with my input genomes? I indexed the samfiles, so I assume it's not about a weird stream sent by samtools.
Thanks & best,
Sebastian