Cluster IndexError #2
Description
Hi
I'm running Panakeia and i encounter and error, i guess is related to clustering, since I also got an error doing it
513357 finished 18243 clusters
Approximated maximum memory consumption: 535M
writing new database
writing clustering information
program completed !
Total CPU time 365.00
Traceback (most recent call last):
File "Clustering.py", line 174, in
main()
File "Clustering.py", line 139, in main
filter_clusters("cdhit90.clstr", "proteins90.fasta")
File "Clustering.py", line 42, in filter_clusters
protein_dict.pop(c)
KeyError: 'CALIBMGJ_00459'
When I try to run the main script this is what i got
python3 Panakeia.py /home/jason/Documentos/Panakeia_vibrio /home/jason/Documentos/Panakeia_vibrio/gff /home/jason/Documentos/Panakeia_vibrio/cdhit90 /home/jason/Documentos/Panakeia_vibrio/vibrio.faa
Traceback (most recent call last):
File "Panakeia.py", line 797, in
main()
File "Panakeia.py", line 779, in main
read_clusters(args.clust, args.rep)
File "Panakeia.py", line 65, in read_clusters
left_locus = re.sub('^ ', "", preid[1])
IndexError: list index out of range
Not sure about rep file requirements or extension, when i use a folder or invoke all files using * i also got an error for every file
python3 Panakeia.py /home/jason/Documentos/Panakeia_vibrio /home/jason/Documentos/Panakeia_vibrio/gff /home/jason/Documentos/Panakeia_vibrio/cdhit90 /home/jason/Documentos/Panakeia_vibrio/faa/*.faa
Panakeia.py: error: unrecognized arguments:
Regards