Errors after running jobscript for cellranger vdj pipeline

Question

[Kimaya]

Hello,

Below is pasted my jobscript to be submitted to run cellranger vdj pipeline on my fasta sample files.

1   #!/bin/bash
2   #PBS -N RED_aregvdj
3   #PBS -q serial
4   #PBS -l nodes=1:ppn=24
5   #PBS -l walltime=03:00:00
6   #PBS -l pmem=3300mb
7   #PBS -m abe

8   cd /home/tek05139/beegfs/PBS_O_WORKDIR/

9   source '/software/cellranger-7.0.1/sourceme.bash'
10  source '/software/cellranger-7.0.1/sourceme.csh'
11  mpiexec -np 24 /software/cellranger-7.0.1/cellranger

12  cellranger vdj --id=red_aregvdj --fastqs=/home/tek05139/beegfs/DZ_081222/outs/fastq_path/AACGCHJM5 --reference=/home/tek05139/beegfs/refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 --sample=1_RED  --localcores=24 --localmem=64

After submitting the job, it runs for few minutes and returns the following error. I do not understand why. Can anyone please help :)

software/cellranger-7.0.1/sourceme.csh: line 6: syntax error near unexpected token `('/software/cellranger-7.0.1/sourceme.csh: line 6: `set SOURCE=($_)'

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Open MPI does not support recursive calls of mpiexec

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I tried adding '_' to my source command after getting this error, but I nevertheless continue getting these errors. As far as I can get, there are two separate errors to be dealt with here. one is to be done with the syntax and the other for the mpiexec

Any help would be highly appreciated

[GenoMax]

cellranger is not MPI-aware software package so you can't use mpiexec to run it. Take out line 11 and try running again.

Do you know if cellranger has been properly configured on your cluster? PBS is not supported by 10x and using cluster mode will need proper configuration by your cluster admins to work (LINK).