Question: Bash not finding file
0
gravatar for mac03pat
22 days ago by
mac03pat10
mac03pat10 wrote:

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

linux bash debian9 • 162 views
ADD COMMENTlink modified 22 days ago • written 22 days ago by mac03pat10
1

Can you show us what you get when you do: for infile in ~/inputs/*.gb; do echo $infile; done?

ADD REPLYlink written 22 days ago by SMK1.3k
(antismash) macpat@Debian9:~$ for infile in ~/inputs/*.gb; do echo $infile; done
/home/macpat/inputs/DQ660910.gbor infile in ~/inputs/*.gb; do echo $infile; done
/home/macpat/inputs/EU872212.gb
/home/macpat/inputs/GU930713.gb
/home/macpat/inputs/GU930714.gb
/home/macpat/inputs/HM180407.gb
/home/macpat/inputs/HM180409.gb
/home/macpat/inputs/HQ823618.gb
/home/macpat/inputs/HQ823619.gb
/home/macpat/inputs/HQ823620.gb
/home/macpat/inputs/HQ823621.gb
/home/macpat/inputs/JN408682.gb
/home/macpat/inputs/JQ340775.gb
/home/macpat/inputs/JX067626.gb
/home/macpat/inputs/JX067627.gb
/home/macpat/inputs/JX232185.gb
/home/macpat/inputs/JX232186.gb
/home/macpat/inputs/JX232187.gb
/home/macpat/inputs/JX232188.gb
/home/macpat/inputs/KJ501919.gb
/home/macpat/inputs/MG777489.gb
/home/macpat/inputs/MG777490.gb
/home/macpat/inputs/MG777491.gb
/home/macpat/inputs/MG777492.gb
/home/macpat/inputs/MG777493.gb
/home/macpat/inputs/MG777494.gb
/home/macpat/inputs/MG777495.gb
/home/macpat/inputs/MG777496.gb
/home/macpat/inputs/MG777497.gb
/home/macpat/inputs/MG777498.gb
/home/macpat/inputs/MG777499.gb
/home/macpat/inputs/MG777500.gb
/home/macpat/inputs/MG777501.gb
/home/macpat/inputs/MG777502.gb
ADD REPLYlink written 22 days ago by mac03pat10
4
gravatar for SMK
22 days ago by
SMK1.3k
Ghent, Belgium
SMK1.3k wrote:

I see. Try again with:

for infile in ~/inputs/*.gb; do antismash $infile --taxon fungi --input-type nucl --knownclusterblast; done
ADD COMMENTlink written 22 days ago by SMK1.3k

Seems to have worked, thank you!. I beleive now I'm running into problems with the package itself. The online version returns results for the same file that I'm trying to run on the downloaded package version of the program. However, the downloaded version is returning me this error:

WARNING 25/05 23:06:49   Error parsing best knowncluster hit; knownclusters array = []. Possibly no significant hits to known biosynthetic gene clusters.
ADD REPLYlink written 22 days ago by mac03pat10

You're welcome. This is already a new question, please consider posting to a new one.

ADD REPLYlink written 22 days ago by SMK1.3k

Not sure why the error appeared but files were output! Good to go, thank you.

ADD REPLYlink written 21 days ago by mac03pat10
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