Entering edit mode
6.7 years ago
Kari Vázquez
•
0
Hello everybody, I´m working with My Taxa for a metagenomic analysis and I had lots of errors when I received the results . I suppose the problem is the database, so my question is: What NCBI database do I need to get the tabular output on the blastp? Thank you for your help :)
Yes. I used the nr database and the error shown is: [11s] Cmd: ["perl", "infile_convert.pl", "-f", "gff2", "-l", "0.75", "-q", "--", "gmhmmp1.out.gff2", "result.tmp2"] > result.tmp3. Cannot find contig for gene gene_1000|GeneMark.hmm|210_aa|-|170900|171532. Exception: Execution failed.
run-job.rb:254:in run_cmd' run-job.rb:154:inmytaxa' run-job.rb:36:in go!' run-job.rb:268:in<main>'
This is the command : blastp -query 1.faa -db nr.03 -out 1.blast -outfmt "6 qseqid sallseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"
Default format for
-outfmt 6
is sseqid, not sallseqid - maybe this is the problem? Try a quick test with