Errors with Mytaxa online program

Question

[Kari Vázquez]

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 :)

Answer 1

[h.mon]

You can get the tabular output with any database. To get tabular output you have just to select tabular output.

But:

1. You didn't describe what errors you get with MyTaxa
2. You didn't describe how you are performing blastp

On the command line, you should use -outfmt 6

[Kari Vázquez]

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"

[h.mon]

Default format for -outfmt 6 is sseqid, not sallseqid - maybe this is the problem? Try a quick test with

blastp -query 1.faa -db nr.03 -out 1.blast -outfmt 6