Cellranger count.srun issues
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21 days ago

Hi very new to bioinformatics and am doing an analysis of single-cell sequencing fastq data from a previously published paper. I downloaded the FASTQ files and put them in their own directory. Then wrote this script based on an example given to me. The error I get is exit code 127 cellranger: command not found.

#!/bin/bash
#SBATCH --job-name=cellranger
#SBATCH --mail-type=END,FAIL
#SBATCH --ntasks=1
#SBATCH --mem=40gb
#SBATCH --cpus-per-task=4
#SBATCH --time=24:00:00
#SBATCH --output=cellrangerProject3.log

source ~/.bashrc
export PATH=/network/rit/misc/scratch/single_cell/cellranger/cellranger=3.0.2:$PATH
cellranger count --id=noinjury1 --transcriptome=/network/rit/misc/scratch/single_cell/refdata-cellranger-mm10-3.0.0  --fastqs=/network/rit/lab/bioinformaticslab/BGonzalez/Project3/Noinjury --sample=noinjury1
cellranger count --id=noinjury2 --transcriptome=/network/rit/misc/scratch/single_cell/refdata-cellranger-mm10-3.0.0  --fastqs=/network/rit/lab/bioinformaticslab/BGonzalez/Project3/Noinjury --sample=noninjury2
cellranger srun • 286 views
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Well, did you make sure cellranger was installed?

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cellranger is for sure installed. A sample script using the same commands just different fastq paths worked fine but for some reason this script will not

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cellranger: command not found.

Are you sure this PATH value is correct /network/rit/misc/scratch/single_cell/cellranger/cellranger=3.0.2? Perhaps there is a bin directory that you missed adding, so the PATH should really be /network/rit/misc/scratch/single_cell/cellranger/cellranger=3.0.2/bin. cellranger executable should be in that directory. I would check on that first.

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The path used has worked on previous scripts but I tried what you said. It still resulted in the same error.

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That does not make logical sense based on error which said command not found. If a prior script worked with same PATH but if this is generating an error then you should verify that the cellranger executable is there. Do you see a file listed if you try ls -lh /network/rit/misc/scratch/single_cell/cellranger/cellranger=3.0.2/bin/cellranger?

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