Output Of Running Hhblits With Multithread

Question

[Schmid]

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!

[Naga]

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

[Schmid]

thank you naga! Prblem solved.