Trimmomatic error: cannot execute binary file: Exec format error
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Entering edit mode
6 weeks ago
mthm ▴ 30

I am trying to run Trimmomatic from a docker container using this piece of command:

docker run -v ~:/home  -v /data:/data quay.io/biocontainers/trimmomatic:0.36--6 trimmomatic PE -trimlog /usr/local/share/trimmomatic-0.36-6/adapters/NexteraPE-PE.fa:2:30:10 | /data/Sample1_R1.fastq.gz /data/Sample1_R2.fastq.gz | Sample1_R1_paired.fastq.gz Sample1_R1_unpaired.fastq.gz Sample1_R2_paired.fastq.gz Sample1_R2_unpaired.fastq.gz

this is the error I recieve

-bash: Sample1_R1_paired.fastq.gz: command not found
-bash: /data/Sample1_R1.fastq.gz: cannot execute binary file: Exec format error
/usr/local/bin/trimmomatic: line 6: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory

I don't have the "sudo" rights and I haven't installed the docker, I am just running it, so where I am wrong?

p.s. the NexteraPE-PE.fa is inside the container's directory and the sample files are in the local directory /data, if it helps. Thanks

adapter trimmomatic fastq • 266 views
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2
Entering edit mode
6 weeks ago

this is unrelated to docker. You put a pipe in your command line

(..) astq.gz | Sample1_R1_paired.fastq.gz (...)

so you shell thinks there is an executable named "Sample1_R1_paired.fastq.gz"

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Thanks that fixed it partially, so I don't get the sample error anymore, but I still get this warning and doesn't start running:

 /usr/local/bin/trimmomatic: line 6: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Usage:
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or:
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or:
       -version
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1
Entering edit mode

it evidently runs in that shows you the usage,

if you are trimming adapters make sure to use the ILLUMINACLIP action as the manual states, right now you are listing the adapters directly at the command line

as for locale:

https://askubuntu.com/questions/162391/how-do-i-fix-my-locale-issue

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