The module gatk4/4.2.6.1 is designed to call the gatk4 in singularity image file via the following command "singularity exec /shared/ifbstor1/software/singularity/images/gatk4-4.2.6.1.sif gatk $@". However, the singularity can not mount the /shared/projects automatically any more although it once works very well. For example, the command "singularity exec /shared/ifbstor1/software/singularity/images/gatk4-4.2.6.1.sif ls /shared/projects/chengw_wgs" will report "cannot access '/shared/projects/chengw_wgs': No such file or directory". The command should be modifed as follow: "singularity exec --bind /shared/projects/chengw_wgs:/shared/projects/chengw_wgs /shared/ifbstor1/software/singularity/images/gatk4-4.2.6.1.sif ls /shared/projects/chengw_wgs", where a manual file path mount is required now.
Hell @Wenxuan
Where to you have this issue ? In the login node or in a compute node ? Maybe you have a jobid ?
Actually I have tried it in the login node and compute node last night but both failed. I can provide the job ID (40941410) of a small demo for your information. I think you can also reproduce this error in the login node using the two commands I mentioned in the previous post.
I do not reproduce the error.
I do not reproduce the error with your account too.
Could you simply try to disconnect/reconnect on the cluster (and try again) ?
I identified the issue: I previously installed Singularity version 3.8.6 and added it to my module configuration file. When I load GATK4, it is using my own installation of Singularity instead of the pre-installed version, which has resulted in a write permission error. I apologize for any confusion this may have caused.