Trinity cannot locate file

I run trinity for my Fastq.gz files and I get error of canot locate file. the files are there if run ls with the path it works. I even copied the files to the same dir and he still cant locate. any suggestions thank you

trinity

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updated 4.1 years ago by iraun 627 • | written 4.1 years ago by galwodow 0

what is the command line + show us the error messages ?

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written 4.1 years ago by Pierre Lindenbaum 17K

Error, cannot locate file:

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written 4.1 years ago by galwodow 0

what is the command line

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written 4.1 years ago by Pierre Lindenbaum 17K

singularity exec -e trinityrnaseq.v2.14.0.simg  Trinity \
         --seqType fq \
         --max_memory 200G \
         --left /beegfs/data/gwodowski/tools/Trinity_snake/PC1_R1_001.fastq.gz,/beegfs/data/gwodowski/$
         --right /beegfs/data/gwodowski/tools/Trinity_snake/PC1_R2_001.fastq.gz,/beegfs/data/gwodowski$
         --CPU 4 \

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updated 4.1 years ago by GenoMax 16K • | written 4.1 years ago by galwodow 0

are those paths visible from singularity ?? https://docs.sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html

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written 4.1 years ago by Pierre Lindenbaum 17K

no, I now checking this thank you

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written 4.1 years ago by galwodow 0

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