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!