cellranger aggr troubleshooting

Question

[jbonarot]

Hello,

I'm trying to merge 3 data sets using the cellranger aggr pipeline. This data contains three libraries (RNA, ADTs, hashtags) from 3 different patients. Each patient sample has 5 different timepoints pooled.

I've run cellranger count on each individual patient (SCY2, SCY3, SCY4) libraries with resulting molecule_info.h5 files.

For cellranger aggr I created a CSV that looks like this...

library_id  molecule_h5
SCY2    /zfs2/tbilliar/shared/JWB/SCY2/SCY2_results/outs/molecule_info.h5
SCY3    /zfs2/tbilliar/shared/JWB/SCY3/SCY3_results/outs/molecule_info.h5
SCY4    /zfs2/tbilliar/shared/JWB/SCY4/SCY4_results/outs/molecule_info.h5

And the following script...

#!/bin/bash
#SBATCH --job-name=SCY_comb
#SBATCH -N 1
#SBATCH --cpus-per-task=16
#SBATCH --mem=250g
#SBATCH -t 2-00:00 # Runtime in D-HH:MM
#SBATCH --output=SCY_comb.out
#SBATCH --mail-type=END
#SBATCH --mail-user=[e-mail]

module load cellranger/5.0.0

cellranger aggr  --id=SCY_comb_results \
                 --csv=SCY_comb_library.csv \
         --normalize=mapped

When I run this, I get the following error in the preflight checks...

[error] Pipestance failed. Error log at:
SCY_comb_results/SC_RNA_AGGREGATOR_CS/PARSE_AGGR_CSV/fork0/chnk0-u77da254fcd/_errors

Log message:
Operation not supported (os error 95)

Has anyone run into this error before? I've reached out to 10x support but haven't heard back yet. Thanks in advance!!

[ATpoint]

Please confirm that you read and tried: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/troubleshooting