Error message when opening the terminal "-bash: /usr/bin/tclsh: No such file or directory"

Je rencontre un probleme pour fonctcionner cellranger,

Il semblerait que la commande tclsh soit défaillante

je reçois ce message d'erreur: "/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory"

En regardant sur internet, il semblerait qu'un réinstallation de via `la commande "sudo apt install tcl" puisse regler le probleme, mais je n'ai pas les droits administrateurs

Comment l'utilisez-vous ?

[glecorguille@clust-slurm-client ~]$ module load cellranger/6.0.0
[glecorguille@clust-slurm-client ~]$ cellranger --version
WARNING: Bind mount '/shared/home/glecorguille => /shared/home/glecorguille' overlaps container CWD /shared/home/glecorguille, may not be available
cellranger cellranger-6.0.0

Le WARNING n'est pas méchant

Merci pour votre réponse,

Je souhaite utiliser la commande mkfastq de cellranger

Ma commande est la suivante:
cellranger mkfastq --id=REIN-CLP --localcores=32 --localmem=200 --run=Novaseq_200622/220620_A00786_0797_AHFHYGDRX2/Data/Intensities/BaseCalls --csv=Novaseq_200622/220620_A00786_0797_AHFHYGDRX2/SampleSheet.csv

Bonjour,

J'ai eu exactement le même problème et j'aurais voulu savoir si vous aviez pu régler le problème ?
Merci beaucoup

Commande :

module load bcl2fastq/2.20.0
module load cellranger/4.0.0

cellranger mkfastq --run=/shared/projects/rna_seq_malaria_induced/scRNA-seq/Run_329_NS500-236_13-10-2020_SM/ --csv=/shared/projects/rna_seq_malaria_induced/scRNA-seq/Run_329_NS500-236_13-10-2020_SM/SampleSheet.csv &>bcl.log

Erreur :

/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
/opt/cellranger-4.0.0/bin
/shared/software/modules/4.6.1/init/bash: line 37: /usr/bin/tclsh: No such file or directory
cellranger mkfastq (cellranger-4.0.0)
Copyright (c) 2020 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 - v4.0.0
2022-12-09 08:28:57 [jobmngr] WARNING: configured to use 226GB of local memory, but only 201.4GB is currently available.
Serving UI at http://cpu-node-27.ifb.local:43817?auth=ws-z5OupV3BpLydLI5Dgog3klorljDrjwMbGrIcvGGU

Running preflight checks (please wait)...

[error] No bcl2fastq found on path. mkfastq requires bcl2fastq v2.17 or greater for RTA version: 2.11.3

2022-12-09 08:28:58 Shutting down.
2022-12-09 08:28:58 Caught signal terminated
2022-12-09 08:28:58 [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 "HFKHNBGXG/HFKHNBGXG.mri.tgz"
For assistance, upload this file to 10x Genomics by running:

cellranger upload <your_email> "HFKHNBGXG/HFKHNBGXG.mri.tgz"

srun: error: cpu-node-27: task 0: Exited with exit code 1