Trimmomatic error: cannot execute binary file: Exec format error
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
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