Question: Bash not finding file
0
gravatar for mac03pat
12 months ago by
mac03pat30
mac03pat30 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 • 379 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by mac03pat30
1

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

ADD REPLYlink written 12 months ago by SMK1.9k
(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 12 months ago by mac03pat30
4
gravatar for SMK
12 months ago by
SMK1.9k
SMK1.9k wrote:

I see. Try again with:

for infile in ~/inputs/*.gb; do antismash $infile --taxon fungi --input-type nucl --knownclusterblast; done
ADD COMMENTlink written 12 months ago by SMK1.9k

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 12 months ago by mac03pat30

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

ADD REPLYlink written 12 months ago by SMK1.9k

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

ADD REPLYlink written 12 months ago by mac03pat30
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