I'm getting the below error when I try to run your sample dataset. I'm using virtualenv to switch between python versions. Any help here would be highly appreciated.
(ENV) anto@kw12957:~$ iRep -f /home/antonycp/Downloads/l_gasseri.fna -s /home/anto/Downloads/l_gasseri.fna-vs-l_gasseri_sample2-shrunk.sam -o /home/anto/Downloads/test.iRep
Traceback (most recent call last):
File "/home/anto/ENV/bin/iRep", line 73, in
thresholds, args['no_gc_correction'], args['t'])
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/iRep.py", line 976, in iRep
genomes, id2g = parse_genomes_fa(fastas, mappings)
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/iRep.py", line 916, in parse_genomes_fa
for seq in parse_fasta(genome):
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/fasta.py", line 19, in iterate_fasta
sequence, formatted = parse_fasta(line, sequence, length)
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/fasta.py", line 32, in parse_fasta
sequence[1].append(line.replace(' ', ''))
IndexError: list index out of range
Hi Chris,
I'm getting the below error when I try to run your sample dataset. I'm using virtualenv to switch between python versions. Any help here would be highly appreciated.
(ENV) anto@kw12957:~$ iRep -f /home/antonycp/Downloads/l_gasseri.fna -s /home/anto/Downloads/l_gasseri.fna-vs-l_gasseri_sample2-shrunk.sam -o /home/anto/Downloads/test.iRep Traceback (most recent call last): File "/home/anto/ENV/bin/iRep", line 73, in
thresholds, args['no_gc_correction'], args['t'])
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/iRep.py", line 976, in iRep
genomes, id2g = parse_genomes_fa(fastas, mappings)
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/iRep.py", line 916, in parse_genomes_fa
for seq in parse_fasta(genome):
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/fasta.py", line 19, in iterate_fasta
sequence, formatted = parse_fasta(line, sequence, length)
File "/home/anto/ENV/lib/python3.6/site-packages/iRep/fasta.py", line 32, in parse_fasta
sequence[1].append(line.replace(' ', ''))
IndexError: list index out of range