I'm running Debian 9 as VM from serial console on Azure.
Link to files I'm attempting to input: https://drive.google.com/open?id=1aIIjWO70clU8u4_gV2X_8c17HmEnqjr_
I was given some code from the help people at antiSMASH. It should iterate through genbank files in a folder and process them with the antiSMASH package:
for infile in inputs/*.gbk; do
antismash $infile --taxon fungi --input-type nucl --knownclusterblast
done
I tried running it while at the directory containing the files, and I tried running it while at the directory containing the folder "inputs" which contains the .gb files:
(antismash) macpat@Debian9:~/inputs$ for infile in inputs/*.gb; do
> antismash $infile --taxon fungi --input-type nucl --knownclusterblast
> done
ERROR 25/05 21:53:00 No sequence file found at 'inputs/*.gb'
This is the email I was sent by the antiSMASH people:
Dear a ntiSMASH user,
For running antiSMASH on many input files, I usually write a loop in bash, like so:
for infile in inputs/*.gbk; do
antismash $infile --your --other-options --here
done
Assuming your input files are in GenBank format and located in a subdirectory of your current directory called "input", antiSMASH will run on all your input files sequentially. I'm aware you asked for "all at once", but as antiSMASH has pretty decent CPU and memory requirements, especially when running ClusterBlast, I would not recommend that.
Best regards, Kai
Can you show us what you get when you do:
for infile in ~/inputs/*.gb; do echo $infile; done?