Bonjour,
impossible de lancer un alignement de scRNAseq au moyen de cellranger, il semble que le module ne reconnaisse pas la dépendance bcl2fastq dont il a besoin
mon script ici :
#!/bin/bash
#SBATCH --job-name=cellranger_CdR
#SBATCH --mem=80GB
#SBATCH --account=fatemapping_ilastik
#SBATCH --cpus-per-task=8
module load cellranger
module load bcl2fastq
cellranger mkfastq --id=tutorial_walkthrough \
--run=/shared/ifbstor1/projects/fatemapping_ilastik/scRNAseq/test/cellranger-tiny-bcl-1.2.0 \
--csv=/shared/ifbstor1/projects/fatemapping_ilastik/scRNAseq/test/cellranger-tiny-bcl-simple-1.2.0.csv
echo 'Job finished' $(date --iso-8601=seconds)
Et le message d'erreur :
/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
/opt/cellranger-6.0.0/bin
/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
cellranger mkfastq (cellranger-6.0.0)
Copyright (c) 2021 10x Genomics, Inc. All rights reserved.
-------------------------------------------------------------------------------
/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Martian Runtime - v4.0.3
2022-06-16 16:38:40 [runtime] Reattaching in local mode.
Serving UI at http://cpu-node-6:44085?auth=T6e-eJLMzY4JVVTRbjQkdedMQArnJeZ2Y8W1UbjmlYA
2022-06-16 16:38:40 [runtime] (reset-partial) ID.tutorial_walkthrough.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT.fork0
.chnk0
2022-06-16 16:38:40 [runtime] (reset-partial) ID.tutorial_walkthrough.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFLIGHT_LOCAL
.fork0.chnk0
2022-06-16 16:38:40 [runtime] Found orphaned local stage: ID.tutorial_walkthrough.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFL
IGHT
2022-06-16 16:38:40 [runtime] Found orphaned local stage: ID.tutorial_walkthrough.MAKE_FASTQS_CS.MAKE_FASTQS.MAKE_FASTQS_PREFL
IGHT_LOCAL
[error] No bcl2fastq found on path. mkfastq requires bcl2fastq v2.17 or greater for RTA version: 1.18.66.4
2022-06-16 16:38:41 Shutting down.
2022-06-16 16:38:42 Caught signal terminated
2022-06-16 16:38:42 [monitor] Caught signal terminated
/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
Saving pipestance info to "tutorial_walkthrough/tutorial_walkthrough.mri.tgz"
For assistance, upload this file to 10x Genomics by running:
cellranger upload <your_email> "tutorial_walkthrough/tutorial_walkthrough.mri.tgz"
Job finished 2022-06-16T16:38:42+0200
Une idée de a source du probleme ?