How To Get Status Update In Ncbi Standalone Blast?

Question

[second_exon]

For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any status message like that? or any other way to send one after another sequence using perl scripts? Many thanks!

[Kumar]

Can u let me know the command for running standalone blast+ for remote EST sequence at NCBI

thanks

Answer 1

[5heikki]

If you chose tabular output (outfmt 6), you can:

cut -f1 outputFile | sort -u | wc -l

To see how many query sequences have been processed. As to how many sequences are being blasted at any given moment with the remote option, the answer is, one.

[Neilfws]

Another Linux shell trick to count sequences in "standard" BLAST output:

grep -c ^Query= outputFile

and if you want that to update every 5 seconds:

watch -n 5 "grep -c ^Query= outputFile"