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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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error while running cellranger vdj pipeline on cluster #207

Closed Ktek28 closed 11 months ago

Ktek28 commented 1 year ago

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=($_)'

Open MPI does not support recursive calls of mpiexec

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

mmokrejs commented 1 year ago

Hi, I did not try vdj mode only count but maybe try to fix your installation first by installing patches from https://github.com/10XGenomics/cellranger/issues/218 and https://github.com/10XGenomics/cellranger/issues/219 if that eventually helps too?

elehnert10x commented 11 months ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.