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Gabaldonlab / perSVade

perSVade: personalized Structural Variation detection
GNU General Public License v3.0
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How to run a module multiple times at the same time? #8

Closed xibeixingchen closed 2 years ago

xibeixingchen commented 2 years ago

Hi,

I have 186 sample, and want to run a module for each sample separately, such as call_small. This was supposed to speed things up. However, a new problem arises when multiple commands are executed and a new error is generated.

INFO: Convert SIF file to sandbox... FATAL: while extracting /home/jiazc/software/persvade.sif: root filesystem extraction failed: failed to copy content in staging file: write /tmp/archive-672565402: no space left on device

How can I solve this problem?

Best, Thanks

MikiSchikora commented 2 years ago

Hi,

Could this be a disk space problem? Maybe removing /tmp/archive-672565402 and re-running solves the issue? If not, maybe you need a computer with more disk. Can you send the full STDERR/STDOUT of one of perSVade's runs to debug?

Best, Miquel Àngel Schikora

xibeixingchen commented 2 years ago

Hi,

Thank you for your professional answers, when I removed /tmp/archive-672565402 and re-running solves the issue. In addition, there does not seem to see full STDERR/STDOUT of one of perSVade's runs, I did not see it in the folder, it should run correctly. perSVade is now mounted under the /tpm/ , can I modify the mounted file through singularity -B ?

Thanks, Best, Zhicheng Jia

MikiSchikora commented 2 years ago

Hi,

Regarding the lack of STDERR/STDOUT for one run, I am not sure of what happened. I have seen that when there are disk errors some files get deleted or empty, which could explain it.

Regarding the mounting, I know that singularity mounts several folders automatically ($HOME and /tmp for sure). Maybe you could mount whatever folder (<folder>) as /tmp by adding -B <folder>:/tmp.

Best, Miquel Àngel Schikora

xibeixingchen commented 2 years ago

Hi,

Thank your professional suggestion, I have solved this issue.

Thanks, Best, Zhicheng Jia