STOmics / SAW

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Suggestion: add --bind options for singularity in stereoPipeline.sh #62

Closed WeipengMO closed 1 year ago

WeipengMO commented 1 year ago

As the data is stored in another directory, it is necessary to mount other directories or files when running. Can the bind option be added to the script?

Tue Aug 22 16:17:58 CST 2023  singularity check: pass, and singularity path is /usr/local/bin/singularity
Tue Aug 22 16:17:58 CST 2023  singularity image file check: file exist and SIF path is /home/weipeng/software/singularity/SAW_6.1.sif
Tue Aug 22 16:17:58 CST 2023 => splitMask, compute CID count and predict the memory of mapping start......
Error, cannot access rawData/mask/FP200009107_E414.barcodeToPos.h5
Command exited with non-zero status 1
        Command being timed: "singularity exec /home/weipeng/software/singularity/SAW_6.1.sif CIDCount -i rawData/mask/FP200009107_E414.barcodeToPos.h5 -s species -g 3"
        User time (seconds): 0.06
        System time (seconds): 0.16
        Percent of CPU this job got: 58%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.39
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 29540
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 43
        Minor (reclaiming a frame) page faults: 2499
        Voluntary context switches: 2338
        Involuntary context switches: 198
        Swaps: 0
        File system inputs: 7496
        File system outputs: 8
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 1
WeipengMO commented 1 year ago

set $SINGULARITY_BIND can fix this.