Error with creating markers using uniref 100: Command '['makeblastdb returned non-zero exit status 1

[Violetta Florova]

Hello everyone!

While running the following code I've got error (the test marers database worked good though)

./shortbred_identify.py --goi adjusted_K00367.fasta --ref  uniref100.fasta --markers K00367markers.faa

subprocess.CalledProcessError: Command '['makeblastdb', '-in', 'uniref100.fasta', '-out', 'tmp724881527618996241/refdb/refdb', '-dbtype', 'prot', '-logfile', 'tmp724881527618996241/refdb.log']' returned non-zero exit status 1

O've got the same error with uniref 90 as well.. probably it's the issue of the path..

I'm new in bioinformatic so I really appreciate any your advice!

Thanks,

Violetta

[Dave Yarmosh]

Hi Violetta,

Have you tried using the makeblastdb command from your command line, instead of doing it through ShortBRED? Something like

makeblastdb -in uniref100.fasta -out uniref.blastdb -dbtype prot

Where your filepaths are set to your preference.

Dave