Demuxafy problems: can't open file 'Demuxalot.py'

[MrLocuace]

Hi @arogozhnikov,

I am trying running the script below. I have both Demuxalot.py and Demuxalot.sif in this dir: /project/PI/USERS/me/czi/data/scrna, which is located upstream of all input files.

!/bin/bash

###########################################

SBATCH --time=34:00:00

SBATCH --partition=PI

SBATCH --account=pi-lb

SBATCH --mem=120G

SBATCH --nodes=1

SBATCH --ntasks=1

SBATCH --cpus-per-task=12

SBATCH --output=/project/PI/USERS/me/czi/data/scrna/demuxalot/demuxalot-%j.out

SBATCH --error=/project/PI/USERS/me/czi/data/scrna/demuxalot/demuxalot-%j.err

###########################################

module load apptainer/1.1.4

cd /project/PI/USERS/me/czi/data/scrna

DIR1=/project/PI/USERS/me/czi/data/scrna BATCH=${1} SAMPLE=$(echo "$BATCH")

SAMPLE=$(echo "$BATCH" | cut -d"_" -f1)

BARCODES=$DIR1/cellranger/${SAMPLE}_OUT/outs/filtered_feature_bc_matrix/barcodes.tsv BAM=$DIR1/cellranger/${SAMPLE}_OUT/outs/possorted_genome_bam.bam INDS=$DIR1/demuxalot/indvs_batch1.txt VCF=$DIR1/souporcell/batch1.MAF0.05.vcf.gz DEMUXALOT_OUTDIR=$DIR1/demuxalot/${SAMPLE}_OUT

apptainer exec --bind $DIR1:/tmp Demuxafy.sif python Demuxalot.py \ -b /tmp/$BARCODES \ -a /tmp/$BAM \ -n /tmp/$INDS \ -v /tmp/$VCF \ -o /tmp/$DEMUXALOT_OUTDIR \ -r True

But I get this error:

/opt/conda/envs/py37/bin/python: can't open file 'Demuxalot.py': [Errno 2] No such file or directory

Please help

[arogozhnikov]

I'd blindly guess that you don't need to --bind anything, and it should work. If not - start with

apptainer exec Demuxafy.sif pwd # show current dir in container
apptainer exec Demuxafy.sif ls # show content of current dir

But if you do want to --bind, your paths inside should be -v /tmp/souporcell/batch1.MAF0.05.vcf.gz, and right now it is /tmp/$DIR1/souporcell/batch1.MAF0.05.vcf.gz ; also script should be python /tmp/Demuxalot.py

I've never tried apptainer, in case advice above does not help, better ask for help from demuxafy authors.

[MrLocuace]

Hi @arogozhnikov, Thank you for your reply. Unfortunately, your suggestions did not work. I get the same error message all the time.

[me@midway3-login3 scrna]$ apptainer exec Demuxafy.sif pwd /home/me [me@midway3-login3 scrna]$ apptainer exec Demuxafy.sif ls R RtmpHkYF2q RtmpM5ugYe RtmpTi73Rg authorized_keys cellranger_count1.sbatch include perl5 thindrives RtmpACNEOR RtmpLYUF84 RtmpMfuEoa Rtmpc673Mn bin customize_env.sh lib share

[arogozhnikov]

yup, so current folder in container clearly does not contain files that you expect it to contain - so you confirmed apptainer does not work as you expect it to.