Question: Output Of Running Hhblits With Multithread
0
gravatar for Schmid
5.6 years ago by
Schmid0
Schmid0 wrote:

Hi,

I'm running HHblits using many different input files using multithread.

multithread.pl '/home/chris/Bioinformatics/Virus/Mimi/*.a3m' 'hhblits -i $file -d /home/chris/Bioinformatics/hhsuite/databases/VacV/VacVdb -o $name.hhr -oa3m /home/chris/Bioinformatics/results/Mimi/$name.a3m -n 2 -norealign -e 1e-3 2>>error.log' -cpu 3

The job is being executed, but no output files generated. From the error.log file I get an error message saying

Error in hhblits: could not open file '/home/chris_schmid/Bioinformatics/results/Mimi//home/chris_schmid/Bioinformatics/VirusProteomes/Mimivirus/sp_Q5URB3_YR187_MIMIV.a3m'

Is it possible to have the reulting a3m-file being written into a directory different from the input directory? Concerning the globbing file expression, is the glob the path pointing at the files I want to query or only each individual a3m-file?

Thank you a lot for your help!

• 1.9k views
ADD COMMENTlink written 5.6 years ago by Schmid0
1

I think this causes your error "/home/chris/Bioinformatics/results/Mimi/$name.a3m", try "$name.a3m" instead

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Naga450

thank you naga! Prblem solved.

ADD REPLYlink written 5.6 years ago by Schmid0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 836 users visited in the last hour