Question: KOBAS2.0 , problems
0
gravatar for maxnest
3.0 years ago by
maxnest10
maxnest10 wrote:

Hello, dear colleagues! My apologies for my English.

I have some problems with installation/starting of kobas2.0 and I hope somebody can help me. Followed the instructions , I installed all packages and programs (pip , biopython, rpy2, pysqlite, ncbi-blast-2.3.0+ (standalone version)), created folders (seq_pep, sqlite3) and copied into them data bases and file with peptides sequences (organism.db and smm.db => sqlite3; smm.pep.fasta => seq_pep). Like in the instruction, I changed file «kobasrc», renamed it to the «.kobasrc» and moved it into the main folder (/Desktop/kobas2.0/).

Yes, I modified PATH and PYTHONPATH, added paths to folders sqlite3, scripts, src, seq_pep. When I start any scripts (run_kobas, annotate) with all options , as results I have only error message :

«…. Bio.Application.ApplicationError: Non-zero return code 2 from '/home/manager/Desktop/ncbi-blast-2.3.0+/bin/blastx -outfmt 5 -query /home/manager/Desktop/DE_results/pwithmar.fasta -db /home/manager/Desktop/kobas2.0-20150126/seq_pep/smm.pep.fasta -num_threads 2', message 'BLAST Database error: No alias or index file found for protein database [/home/manager/Desktop/kobas2.0-20150126/seq_pep/smm.pep.fasta] in search path [/home/manager:/var/lib/blastdb:]»

or

«Traceback (most recent call last): File "/home/manager/Desktop/kobas2.0-20150126/scripts/identify.py", line 3, in <module> ; from kobas.scripts import identify ; File "/home/manager/Desktop/kobas2.0-20150126/src/kobas/scripts/identify.py", line 70, in <module> abbr, idmapping = annot.get_args(fg_handle); File "/home/manager/Desktop/kobas2.0-20150126/src/kobas/annot.py", line 40, in get_args return first_line.split()[0][2:], idmapping ; IndexError: list index out of range»

How I understand, problem with databases or paths. Am I right? Shame on me, if I don’t see obvious solution! =(

paths kobas transcriptome • 1.8k views
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