#5 blastp issue

[Calvin Kim]

We installed ConsPred, but are experiencing issues running the 11arun_blast.sh script. Applying Protein Blast on a tmp file during an annotation run produces:

*USAGE
blastp [-h] [-help] ...

DESCRIPTION
Protein-Protein BLAST 2.2.29+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Argument "task". Illegal value, expected Permissible values: 'blastp' 'blastp-short' 'deltablast' : 'blastp-fast'**

The above output appears whenever blastp is run.

[Thomas Rattei]

Hi,
please check the contents of your conspredProperties.txt file. It should contain a line like

CONSPRED_BLAST_TASK=blastp-fast

Please check if your modifications in conspredProperties.txt are without errors (use diff to compare a modified version of conspredProperties.txt with the original one),

Best,
Thomas

[Thomas Rattei]

Have just recognized that this particular error is due to the ncbi blast+ version you are using. 2.2.29 seems to not support the blastp-fast task setting (although the error message claims so). So, either switch to a newer blast+ (2.3.0 works well), or change the conspredProperties.txt setting to:

CONSPRED_BLAST_TASK=blastp

best,
Thomas

[Calvin Kim]

Fantastic. I updated BLAST and it works much more smoothly now. Thank you!