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davek44 / Glimmer-MG

Gene prediction in metagenomic sequences using Glimmer augmented by phylogenetic classification and clustering
http://www.cbcb.umd.edu/software/glimmer-mg
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Glimmer error #2

Open ghoshal opened 8 years ago

ghoshal commented 8 years ago

Hi,

Whenever I run glimmer-mg.py, I am getting this error

Scanning query lengths...done. [Sat Oct 31 14:21:10 PDT 2015]

Reading IMM list...done. [Sat Oct 31 14:21:10 PDT 2015]

Creating reverse complement of seqs_240471.fa...done. [Sat Oct 31 14:21:10 PDT 2015]

Loading taxonomy...done. [Sat Oct 31 14:21:10 PDT 2015]

Scoring reads with Phymm...rm: cannot remove tempFwd_seqs_240471_fa.txt': No such file or directory rm: cannot removetempRev_seqs_240471_fa.txt': No such file or directory rm: cannot remove `errFile_seqs_240471_fa.txt': No such file or directory done. [Sat Oct 31 14:21:12 PDT 2015]

Traceback (most recent call last): File "/home/biba/data/glimmer-mg/scripts/glimmer-mg.py", line 699, in main() File "/home/biba/data/glimmer-mg/scripts/glimmer-mg.py", line 51, in main (sequence_classes,sequence_scores) = parse_phymm(sequence_file, options.top_hits, options.ignore) File "/home/biba/data/glimmer-mg/scripts/glimmer-mg.py", line 599, in parse_phymm sequence_top_scores[seq] = sequence_scores[s][0][0] IndexError: string index out of range

Please help.

Thanks,

Bibaswan

davek44 commented 8 years ago

NCBI appears to have changed the URL used by Phymm to grab the bacterial taxonomy. If you replace .scripts/.taxonomyInfo/0_getNCBIpages.pl with the one that I just committed into the directory _phymmpatch, it should work again. I modified the install script, too. Try reinstalling phymm, and then testing Glimmer.