SAW ipr2img failed - Githubissues

          running code

echo `date` "=> image processing and registration start......."
export HDF5_USE_FILE_LOCKING=FALSE
dataDir='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010'

imageTarFile='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/rawData/musBrain_WK010/ImageStudio_QC/D03257E614_20240822_114652/D03257E614_SC_20240822_114652_3.0.4.tar.gz'

iprFile='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/rawData/musBrain_WK010/ImageStudio_QC/D03257E614_20240822_114652/D03257E614_SC_20240822_114652_3.0.4.ipr'

#iprFile='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010/03.register/manual_ipr/D03257E614_SC_20240925_111918_3.0.4.ipr'

registJson='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010/03.register/manual_register/20240925093324.regist.json'

imgTarDIR=$(dirname $imageTarFile)
iprDIR=$(dirname $iprFile)
SN='D03257E614'

sif='/xskydata/apps/singularity/SAW/SAW_7.1.sif'

export SINGULARITY_BIND=$outDir,$imgTarDIR,$iprDIR,$dataDir

cp -rf ${iprFile} ${dataDir}/03.register/${SN}.reregist.ipr

offsetX=`cat ${registJson} | sed 's/,/\n/g' | grep "offsetX" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
offsetY=`cat ${registJson} | sed 's/,/\n/g' | grep "offsetY" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
flip=`cat ${registJson} | sed 's/,/\n/g' | grep "flip" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
rotate=`cat ${registJson} | sed 's/,/\n/g' | grep "rotate" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
isTunedStr=`cat ${registJson} | sed 's/,/\n/g' | grep "isTuned" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
extrude_x=`cat ${registJson} | sed 's/,/\n/g' | grep "extrude_x" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
extrude_y=`cat ${registJson} | sed 's/,/\n/g' | grep "extrude_y" | sed 's/:/\n/g' | sed '1d' | sed 's/}//g'|sed 's/"//g'`
if [[ isTunedStr == 'true' ]];then isTuned='True';else isTuned='False';fi

#/usr/bin/time -v singularity exec ${sif} manualRegister \
#   -i ${dataDir}/03.register/manual_register \
#   -c ${dataDir}/03.register/${SN}.reregist.ipr \
#   -v ${dataDir}/02.count/${SN}.raw.gef  \
#   -f $flip \
#   -r $rotate \
#   -o $offsetX $offsetY \
#   -s $extrude_x $extrude_y \
#   -a $isTuned \
#   -p ${dataDir}/03.register/aa

out_iprFile=$(find ${dataDir}/03.register/ -maxdepth 1 -name \*.ipr | head -1)
/usr/bin/time -v singularity exec ${sif} imageTools ipr2img \
    -i ${imageTarFile} \
    -c ${out_iprFile}  \
    -d tissue cell \
    -r True \
    -o ${dataDir}/03.register/

error message

Wed Sep 25 14:34:26 CST 2024 => image processing and registration start.......
WARNING: While bind mounting '/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/rawData/musBrain_WK010/ImageStudio_QC/D03257E614_20240822_114652:/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/rawData/musBrain_WK010/ImageStudio_QC/D03257E614_20240822_114652': destination is already in the mount point list
Namespace(conf='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010/03.register/D03257E614.reregist.ipr', func=<function ipr2img at 0x1499caf86ca0>, input='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/rawData/musBrain_WK010/ImageStudio_QC/D03257E614_20240822_114652/D03257E614_SC_20240822_114652_3.0.4.tar.gz', module=['tissue', 'cell'], output='/xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010/03.register/', register=True) []
[INFO 20240925-14-34-36 p925703 tar_decompress ipr_to_image.py:294] Extract files from tar.gz file completed.
[INFO 20240925-14-34-36 p925703 main ipr_to_image.py:632] Use the RippleStitch stitching algorithm to calculate the stitching coordinates for stitching.
[INFO 20240925-14-34-38 p925703 main ipr_to_image.py:728] Save ssDNA_fov_stitched.tif success.
[WARN 20240925-14-34-38 p925703 main ipr_to_image.py:735] Failed to generate transform_template.txt template.
[ERRO 20240925-14-34-38 p925703 main ipr_to_image.py:742] SAW-A40704:    Automatic registration or hand registration has not been completed, registration cannot be done, ManualState group not in ipr file.
Traceback (most recent call last):
  File "imagetools-1.7.6/main.py", line 105, in <module>
  File "imagetools-1.7.6/main.py", line 101, in main
  File "imagetools-1.7.6/main.py", line 18, in ipr2img
  File "imagetools-1.7.6/ipr_to_image/ipr_to_image.py", line 234, in __init__
  File "imagetools-1.7.6/ipr_to_image/ipr_to_image.py", line 745, in main
Exception: SAW-A40704:    Automatic registration or hand registration has not been completed, registration cannot be done, ManualState group not in ipr file.
Command exited with non-zero status 1
    Command being timed: "singularity exec /xskydata/apps/singularity/SAW/SAW_7.1.sif imageTools ipr2img -i /xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/rawData/musBrain_WK010/ImageStudio_QC/D03257E614_20240822_114652/D03257E614_SC_20240822_114652_3.0.4.tar.gz -c /xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010/03.register/D03257E614.reregist.ipr -d tissue cell -r True -o /xskydata/project/spatialTranscriptomics/2024/Q3/spatial_transcript_mus.2024.9.23/QC/bgi/WK010/03.register/"
    User time (seconds): 15.08
    System time (seconds): 70.35
    Percent of CPU this job got: 718%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:11.89
    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): 1087032
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 1431
    Minor (reclaiming a frame) page faults: 925284
    Voluntary context switches: 39931
    Involuntary context switches: 100151
    Swaps: 0
    File system inputs: 199646
    File system outputs: 1635992
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 1

QC fail

what should I do.

Originally posted by @lvmt in https://github.com/STOmics/SAW/issues/95#issuecomment-2373164110

STOmics / SAW

SAW ipr2img failed #151