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Sydney-Informatics-Hub / RNASeq-DE

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fastqc_run_parallel.pbs returns sed error #3

Open NJNataren opened 7 months ago

NJNataren commented 7 months ago

Hi I am having issues running the fastqc_run_parallel.pbs script on Gadi, the job fails when queued and returns the following error. I am working on Ubuntu 22.04.4 LTS.

sed: can't read ./Inputs/fastqc.inputs: No such file or directory

I have run the fastqc_make_input.sh successfully to generate the following within /Inputs/fastqc.inputs: ../Batch_1/ERR204943_2.fastq.gz,../Batch_1/_fastQC,./Logs/fastQC/test/Batch_1/ERR204943_2.log,1,875404 ../Batch_1/ERR204943_1.fastq.gz,../Batch_1/_fastQC,./Logs/fastQC/test/Batch_1/ERR204943_1.log,1,857696

It appears that the file in question has the required persmission:

-rwxr-xr-x 1 nn8573 bt64 206 Feb 28 15:41 fastqc.inputs

Any guidance would be appreciated.

nandan75 commented 6 months ago

Hi @NJNataren

Are you still encountering this error? If so I will look into it from my side sometime today/tomorrow.

Nandan

NJNataren commented 6 months ago

Hi @nandan75 Sorry, I meant update. This was solved by adding to the .pbs:

PBS_O_WORKDIR=/path/to/scripts cd ${PBS_O_WORKDIR}

I have set everything up correctly in terms of directories, but still needed to set the PBS_O_WORKDIR to run the script, then the relative paths worked. Easy fix at least.

nandan75 commented 6 months ago

@NJNataren

Great good to know. We will try and incorporate the fix in the future version and push it to main branch.

regards,

Nandan

calizilla commented 5 months ago

This is because the set -e command needs to come after the PBS directives. fastqc_run_parallel.pbs will complete without adding the PBS_O_WORKDIR command (this is covered by #PBS -l wd) IF the set -e command is in the correct place. I have created an issue to fix this for all parallel scripts https://github.com/Sydney-Informatics-Hub/RNASeq-DE/issues/7