search

wbaopaul / scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
MIT License
70 stars 24 forks source link

Issue with executable file not found in $PATH #47

Closed gaelcge closed 2 years ago

gaelcge commented 3 years ago

Hi Not sure what I am doing wrong so I am asking for help. I have pull the singularity sif file on our hpc cluster but I got : FATAL: " ": executable file not found in $PATH.

I am using singularity 3.6 from /opt/software/singularity-3.6/bin/singularity Here is the sif file as seen with singularity sif header scatac-pro_latest.sif Launch: #!/usr/bin/env run-singularity Magic: SIF_MAGIC Version: 01 Arch: amd64 ID: 8d6d707d-e1df-482e-a836-0abde829829d Ctime: 2021-07-12 14:41:02 +0000 UTC Mtime: 2021-07-12 14:41:02 +0000 UTC Dfree: 45 Dtotal: 48 Descoff: 4096 Descrlen: 27KB Dataoff: 32768 Datalen: 5GB

Thanks for your help.

wbaopaul commented 3 years ago

Can you post the full command you have used and the full error message? Thanks.

gaelcge commented 3 years ago

Thanks This is the command to pull the container =

singularity pull -F docker://wbaopaul/scatac-pro:latest

WARN[0000] "/run/user/3045930" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/3045930: no such file or directory: Trying to pull image in the event that it is a public image. INFO: Converting OCI blobs to SIF format INFO: Starting build... WARN[0001] "/run/user/3045930" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/3045930: no such file or directory: Trying to pull image in the event that it is a public image. WARN[0002] "/run/user/3045930" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/3045930: no such file or directory: Trying to pull image in the event that it is a public image. Getting image source signatures Copying blob a4a2a29f9ba4 done
.... Writing manifest to image destination Storing signatures 2021/07/12 07:32:10 info unpack layer: sha256:a4a2a29f9ba48efd3d2075f395538b2eec56fb1bedfb7aecf5e54174446f9e2a ... 2021/07/12 07:35:20 warn rootless{usr/local/bin/bedops/bin/bam2bed} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" ... INFO: Creating SIF file...

ls -la 5453565952 Jul 12 07:41 scatac-pro_latest.sif

Then here the exec command =

singularity exec --bind $HOME --cleanenv -H $workingpath $SCRATCH/scatac-pro_latest.sif \ scATAC-pro -s demplx_fastq \ -i $fastqpath/pe1_fastq.gz,$fastqpath/pe2_fastq.gz,$fastqpath/index_fastq.gz \ -c $workingpath/configure_user.txt

the error message was coming after singularity exec =

FATAL: " ": executable file not found in $PATH

then

bash: scATAC-pro: command not found

I had the same issue when pulling the sif file into my project directory (in case it was due to having pull the sif file into scratch) Thanks Gael

wbaopaul commented 3 years ago

I think some of your bash varibles may not exist that caused the error. Can you double check any typo for the values of those variables or you may use the full path instead of those variable? Or, some time $fastqpath/pe1_fastq.gz should be wrote as ${fastqpath}/pe1_fastq.gz to aviad potential issues.

Hope it helps. Thanks.

wbaopaul commented 2 years ago

Close this issue since it's inactive for more than 3 months