huangnengCSU/compleasm

Protein IndexError: list index out of range

gotouerina opened this issue · 4 comments

gotouerina commented

Command: compleasm.py protein -p Minous.pep.fa -l mammalia -t 50 -o minous -L /home/106public/software/compleasm/mb_downloads

Searching for hmmsearch in the path where compleasm.py is located
Searching for hmmsearch in the current execution path
Searching for hmmsearch in $PATH
Traceback (most recent call last):
File "/home/106public/software/compleasm/compleasm.py", line 2715, in
main()
File "/home/106public/software/compleasm/compleasm.py", line 2711, in main
args.func(args)
File "/home/106public/software/compleasm/compleasm.py", line 2512, in protein_fun
pr.run()
File "/home/106public/software/compleasm/compleasm.py", line 2276, in run
query_name = line[3]
IndexError: list index out of range

gotouerina commented

I meet this problems several times, and what will cause this?

huangnengCSU commented

Hi,

The problem seems to occur during the parsing of the hmmsearch output. Please run the script I provided using python compleasm.py to identify which hmmsearch output file is problematic, and then display the contents of that file here.
compleasm_Issue40.zip

gotouerina commented

Hi I used the compleasm.py in your zip and this time found no error!

gotouerina commented

here is the log
Searching for hmmsearch in the path where compleasm.py is located
Searching for hmmsearch in the current execution path
Searching for hmmsearch in $PATH

S:89.50%, 8257
D:4.70%, 434
F:2.58%, 238
M:3.22%, 297
N:9226