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zamboni-lab / SLAW

Scalable and self-optimizing processing workflow for untargeted LC-MS
GNU General Public License v2.0
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singularity error #37

Open Sunshine318 opened 4 months ago

Sunshine318 commented 4 months ago

I had successfully run it on singularity in past so i am not sure what is this issue if the new image has a bug ?

singularity run -C -B /nfs/turbo/umms-brcfmetab-project/tanusoni/test/output_slaw:/output -B /nfs/turbo/umms-brcfmetab-project/tanusoni/test/positive:/input slaw.sif

2024-07-09|11:04:31|INFO: Total memory available: 129164 and 72 cores. The workflow will use 1819 Mb by core on 71 cores. 2024-07-09|11:04:31|INFO: Guessing polarity from file:20200227-EX01010-A003-IN0028-S00044243-PM3118-P.mzML 2024-07-09|11:04:40|INFO: Polarity detected: positive 2024-07-09|11:04:42|INFO: STEP: initialisation TOTAL_TIME:10.77s LAST_STEP:10.77s 2024-07-09|11:04:43|INFO: 0 peakpicking to do. /run_workflow.sh: line 13: 16 Killed python3 /wrapper_docker.py

htmonkey commented 3 months ago

It seems that you are rerunning on top of a previous execution. Is the output folder empty? Rerun with -e LOGGING=DEBUG. to obtain more information.

Sunshine318 commented 3 months ago

log_docker_stable_version.docx I get the same error with folder being empty . I cant do logging=debug because I am running on singularity. I tried the same in docker and dont get final matrices ,fused file or msms.I have attached docker output.

singularity run -C -B output_slaw:/output -B /nfs/turbo/umms-brcfmetab-project/tanusoni/data/metabolomics/Starr_County_All/EX01010/out_path:/input slaw.sif -d 2024-08-02|14:11:18|INFO: Total memory available: 96463 and 72 cores. The workflow will use 1358 Mb by core on 71 cores. 2024-08-02|14:11:18|INFO: Guessing polarity from file:20230320-EX01010-A003-IN0028-S00044236-PM3203-P.mzML 2024-08-02|14:11:33|INFO: Polarity detected: positive 2024-08-02|14:11:34|INFO: STEP: initialisation TOTAL_TIME:15.97s LAST_STEP:15.97s 2024-08-02|14:11:36|INFO: 140 peakpicking to do. /run_workflow.sh: line 13: 16 Killed python3 /wrapper_docker.py