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STOmics / SAW

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Manual Registration Part 2 Error #80

Closed raforsyth closed 4 months ago

raforsyth commented 10 months ago

I've successfully run the first part of the two part SAW pipeline in version 7.0 with manual image registration. However I'm running into a problem with the second part. I run the following code with the recommended specifications.

bash stereoPipeline_V7.0_manual_part2.sh \
    -SN "D01871D6" \
    -dataDir ${dataDir} \
    -speciesName "homoSapien" \
    -tissueType "sarcoma" \
    -registJson ${json}\
    -outDir "${outDir}" \
    -refIndex "$referenceDir/STAR" \
    -imageRecordFile ${ipr} \
    -imageCompressedFile ${tarball} \
    -sif "$sawDir/SAW_7.0.sif" \
    -threads 16 \
    -doCellbin Y \

I am then given the following output

Wed Nov 22 17:03:48 CET 2023  singularity check: pass, and singularity path is /bin/singularity
Wed Nov 22 17:03:48 CET 2023  singularity image file check: file exist and SIF path is SAW_7.0.sif
Wed Nov 22 17:03:48 CET 2023 => tissueCut start.......
[2023-11-22 17:03:50]   SAW-A50001:  The parameter --sn must be given correctly

I'm deeply confused, since if I add an echo command for the ${SN} variable in stereoPipeline_V7.0_manual_part2.sh and the stereoPipeline_V7.0_manual_part1.sh while I run them, I get the same output. So it is getting my sample ID correctly but can't seem to use it in the singularity container properly.

What is going on?

TheSallyGardens commented 10 months ago

Hi! You may have used the wrong parameter for stereoPipeline_V7.0_manual_part2.sh.https://github.com/STOmics/SAW/blob/main/Scripts/stereoPipeline_v7.0_manual_part2.sh

raforsyth commented 9 months ago

I'm not sure what problem the parameter would be, I can successfully run the full pipeline with the same parameters. But when I run with manual image registration it kicks up this issue. I have found that in part 1 output, I have a warning that I didn't spot before when it runs img2ipr I get the following error: [INFO 20231202-21-46-10 p144432 tar_decompress ipr_to_image.py:294] Extract files from tar.gz file completed. [INFO 20231202-21-46-12 p144432 main ipr_to_image.py:728] Save ssDNA_fov_stitched_transformed.tif success. [WARN 20231202-21-46-12 p144432 main ipr_to_image.py:735] Failed to generate transform_template.txt template.

TheSallyGardens commented 9 months ago

Sorry, I have rerun stereoPipeline_V7.0_manual_part2.sh script, unable to reproduce your error ):.Please carefully check your input.