compressed blast num_threads value

[BurntSushi]

It should be set to the value of the -p switch.

We could parse the arguments given after --blast-args, but I'd rather stick to our simple solution: don't touch them.

[nsarode]

Just one more observation. I face this issue not only during compression, but also in case of blastp. It appears that irrespective of what value I give using -p switch, the program attempts to use all the cores available on the machine (24, 64 etc). This kinda sucks when you are submitting jobs to a shared cluster .... jobs get killed within mins :(

[BurntSushi]

@nsarode Upon further inspection, I'm not actually able to re-create this problem. Here is an example I ran:

[andrew@Serval cablastp] cablastp-search -p 2 ./s288c ./data/test.fasta > /dev/null
Opening database in ./s288c...
        Opening compressed database...
        Done opening compressed database.
        Opening coarse database...
        Done opening coarse database.
Done opening database in ./s288c.

Blasting query on coarse database...
blastp -db s288c/blastdb-coarse -num_threads 2 -outfmt 5 -dbsize 3020248
Decompressing blast hits...
Blasting query on fine database...
blastp -subject /tmp/cablastp-fine-fasta447385406 -dbsize 3020248 -num_threads 2

Note the -p 2, which causes the -num_threads 2 option in both of the blastp commands.

[BurntSushi]

Aha! I've figured it out. I went back to the other issue and noticed you were using this command:

~/path/to/capblast/cablastp-search path/database query_file --p="4" --blast-args -max_target_seqs 10 -num_threads 4 -out out.blast -outfmt '6 qseqid sseqid pident qcovs length mismatch qstart qend sstart send evalue bitscore stitle'

But the usage documentation says:

Usage: cablastp-search [flags] database-directory query-fasta-file [--blast-args BLASTP_ARGUMENTS]

Notice that the flags (except for --blast-args) have to come before the positional arguments. Sorry about that!

I've committed an update so that if you give cablastp-search too many positional arguments (which is how your --p="2" was interpreted), then it will exit with a usage error.

In sum, change your command to this:

~/path/to/capblast/cablastp-search -p 4 path/database query_file --blast-args -max_target_seqs 10 -out out.blast -outfmt '6 qseqid sseqid pident qcovs length mismatch qstart qend sstart send evalue bitscore stitle'

[BurntSushi]

Note that if you have Go installed (and your GOPATH is set, e.g., export GOPATH=$HOME/go), you can update your cablastp binaries by simply running:

go get -u github.com/BurntSushi/cablastp/...

Or I can bug @ndaniels to update the official binaries. :-)

[ndaniels]

I will update the binaries. This is the problem with binary releases :)

Sent from my iPhone

On Nov 14, 2013, at 1:00 PM, Andrew Gallant notifications@github.com wrote:

Note that if you have Go installed, you can update your cablastp binaries by simply running go get -u github.com/BurntSushi/cablastp/....

Or I can bug @ndaniels to update the official binaries. :-)

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Reply to this email directly or view it on GitHub.

[nsarode]

Got it ! I assumed that the order wasn't crucial and that flags would be recognized on the basis of -- before them. Thanks 👍