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I can not get the TRACKLINE in my .stereo file generating from SAW COUNT #163

Open laomaizi-beagle opened 3 weeks ago

laomaizi-beagle commented 3 weeks ago

Dear Auther, I got an issue,when I finished my SAW COUNT pipeline,I find my image QCfial and I want to adjust it in the StereoMap,but after I upload tha image (tif format) and then upload the .stereo, but not like the example given by StereoMap guidelines, I can not find TRACKLINE in my screen ,what should I do ? what is wrong with my .stereo

Many thanks!

Clouate commented 3 weeks ago

@laomaizi-beagle Hi, do you mean that after you clicked "Chip tracklines", you found that the yellow tracklines were not displayed like the guidelines? If so, it is normal because this is an image that failed QC. Yellow tracklines will not be displayed in current version of software, and you could register the image according to the tissue morphology. If you are saying that you cannot see track lines in the microscope image, it may be that the image is too dark. It can be adjusted through the image adjustment button on the upper of toolbar. If the track line cannot be seen even after this, it means that the track line was not captured when taking pictures under the microscope. It can also be registered based on the tissue morphology.

laomaizi-beagle commented 3 weeks ago

Hi! in Stereo -map I can not even click the TRACKLINE button, which is forbid me. And I set the light to highest ,it also not work .so what can I do to make my image pass the QC? And the file folder IMAGE content generating from SAW count are as follows:

image]$ tree . └── bin1_img_tissue_cut.tif

thank you very much!

Clouate commented 3 weeks ago

This is normal, because your image QC failed, which means that your microscope image has poor quality for tracklines. It is recommended to adjust the microscope when taking subsequent photos. For this image, if you really can't see the traklines, you don't need to pay attention to tracklines. It is recommended that you could align according to the tissue morphology on the image and the tissue morphology of the expression heat map.

laomaizi-beagle commented 3 weeks ago

hi,i adjust my image without trackline try my best,and run a realign pipeline ,unfortunately,my image did not pass the image QC,and i have no idea how can i solve this issue

Clouate commented 3 weeks ago

hi,i adjust my image without trackline try my best,and run a realign pipeline ,unfortunately,my image did not pass the image QC,and i have no idea how can i solve this issue

Hi, after StereoMap-Image Proceesing, it will output a new tar.gz, did you input that new tar.gz into saw realign? If so, but the realign output (outs/image) still has no image result, could you provide pipelines-log/log and STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register?

laomaizi-beagle commented 3 weeks ago

pipelines-log/log: Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Job stats: job count

all 1 anno 1 cellcut 1 map 1 merge 1 micro 1 register 1 report 1 saturation 1 spatialcluster 1 tissuecut 1 tissuecut_micro 1 visualization 1 total 13

Select jobs to execute...

[Wed Oct 30 14:23:39 2024] rule map: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_1.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_10.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_11.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_12.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_13.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_14.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_15.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_16.fq.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/fastqs/DP8480011963TR_L01_100_2.fq.gz, 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/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat threads: 24 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_splitmask/splitBcBin -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/mask/D03254G212.barcodeToPos.h5 -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin -t 24 -s 2 -p 2_25 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map 2>&1 /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/01.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/02.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/03.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/04.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/05.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/06.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/07.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/08.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/09.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/10.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/11.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/12.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/13.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/14.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/15.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin/16.D03254G212.barcodeToPos.bin -s toad -g 5G >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/SAW_soft/saw-8.0.2/lib/bcstar/bcSTAR --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --sysShell /bin/bash --limitBAMsortRAM 63168332971 --limitOutSJcollapsed 10000000 --limitIObufferSize=280000000 --outBAMsortingBinsN 50 --readNameSeparator " " --genomeDir /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/STAR --runThreadN 24 --outFileNamePrefix /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map [Wed Oct 30 16:08:07 2024] Finished job 4. 1 of 13 steps (8%) done Select jobs to execute...

[Wed Oct 30 16:08:08 2024] rule anno: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/mask/D03254G212.barcodeToPos.h5, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.bcPara output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/log_anno jobid: 6 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/performance_anno reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara threads: 24 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_count/Bam2Gem -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Aligned.sortedByCoord.out.bam -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam -a /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/reference/transcriptome/genes/toad_ana.gtf -s /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat -e /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef --sat_file /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212_raw_barcode_gene_exp.txt --umi_on --umi_len 10 --save_lq --save_dup --sn D03254G212 -c 24 umi_filter --mask /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/mask/D03254G212.barcodeToPos.h5 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/log_anno 2>&1 [Wed Oct 30 17:35:27 2024] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute...

[Wed Oct 30 17:35:27 2024] rule register: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register jobid: 5 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/performance_register reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat threads: 24 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/register/register/main.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/image/D03254G212_SC_20241030_141229_4.0.1.tar.gz -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE --sn D03254G212 -v /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef --gpu -1 --core 24 -w True >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register 2>&1 [Wed Oct 30 17:36:07 2024] Finished job 5. 3 of 13 steps (23%) done Select jobs to execute...

[Wed Oct 30 17:36:07 2024] rule micro: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/micro_flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_micro jobid: 12 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_micro reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/micro_flag; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat threads: 10 resources: tmpdir=/tmp

[Wed Oct 30 17:36:07 2024] rule merge: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/mask/D03254G212.barcodeToPos.h5, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_merge jobid: 3 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/performance_merge reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt threads: 10 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_merge/mergeBcCount -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt -m /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/mask/D03254G212.barcodeToPos.h5 -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt -t 10 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_merge 2>&1 [Wed Oct 30 17:36:09 2024] Finished job 12. 4 of 13 steps (31%) done [Wed Oct 30 17:36:13 2024] Finished job 3. 5 of 13 steps (38%) done Select jobs to execute...

[Wed Oct 30 17:36:13 2024] rule tissuecut: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut jobid: 2 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_tissuecut reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag threads: 10 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt --sn D03254G212 -O Transcriptomics -d -t 10 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 /share/home/lvbin/SAW_soft/saw-8.0.2/lib/geftools/bin/geftools bgef -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.qcfail.gef -O Transcriptomics -b 1,5,10,20,50,100,150,200 -t 1 >>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 [Wed Oct 30 17:37:30 2024] Finished job 2. 6 of 13 steps (46%) done Select jobs to execute...

[Wed Oct 30 17:37:30 2024] rule saturation: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_saturation jobid: 10 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/performance_saturation reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat resources: tmpdir=/tmp

[Wed Oct 30 17:37:30 2024] rule tissuecut_micro: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/micro_flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut_micro jobid: 11 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_tissuecut_micro reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/micro_flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef threads: 10 resources: tmpdir=/tmp

[Wed Oct 30 17:37:30 2024] rule cellcut: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_cellcut jobid: 7 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_cellcut reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat resources: tmpdir=/tmp

[Wed Oct 30 17:37:30 2024] rule spatialcluster: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/log_spatialcluster jobid: 9 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/performance_spatialcluster reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_spatialcluster/spatial_cluster.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -s 200 -r 1.0 -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/log_spatialcluster 2>&1 /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_saturation/saturation -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212_raw_barcode_gene_exp.txt --tissue /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT --bcstat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat --summary /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_saturation 2>&1 [Wed Oct 30 17:37:31 2024] Finished job 11. 7 of 13 steps (54%) done [Wed Oct 30 17:37:32 2024] Finished job 7. 8 of 13 steps (62%) done [Wed Oct 30 17:37:49 2024] Finished job 10. 9 of 13 steps (69%) done [Wed Oct 30 17:37:56 2024] Finished job 9. 10 of 13 steps (77%) done Select jobs to execute...

[Wed Oct 30 17:37:56 2024] localrule report: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_report jobid: 8 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/performance_report reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/report_v3/v4/main.pyc -m /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat -a /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Log.final.out -g /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat -l /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat -n /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -d /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad -t /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json -b /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_200x200_MID_gene_counts.png -v /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_200x200_MID_gene.png -c /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_200x200_MID_gene_DNB.png --bin20violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_20x20_MID_gene.png --bin20MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_20x20_MID_gene_DNB.png --bin20Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_20x20_MID_gene_counts.png --bin50violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_50x50_MID_gene.png --bin50MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_50x50_MID_gene_DNB.png --bin50Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_50x50_MID_gene_counts.png --bin100violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_100x100_MID_gene.png --bin100MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_100x100_MID_gene_DNB.png --bin100Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_100x100_MID_gene_counts.png --bin150violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_150x150_MID_gene.png --bin150MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_150x150_MID_gene_DNB.png --bin150Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_150x150_MID_gene_counts.png --pipelineVersion 8.0.2 -s Toad_Gland2 --species toad --tissue gland --reference toad -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT --qc_metrics /share/home/lvbin/SAW_soft/saw-8.0.2/config/Metrics_default.xlsx --squareBinMarker /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/bin200_marker_features.csv >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_report 2>&1 [Wed Oct 30 17:38:01 2024] Finished job 8. 11 of 13 steps (85%) done Select jobs to execute...

[Wed Oct 30 17:38:01 2024] rule visualization: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz.md5 jobid: 1 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/performance_visulization reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz.md5; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Select jobs to execute... /share/home/lvbin/SAW_soft/saw-8.0.2/lib/geftools/bin/geftools bgef -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization/D03254G212.gef -O Transcriptomics -b 1,5,10,20,50,100,150,200 -t 1 [Wed Oct 30 17:38:39 2024] Finished job 1. 12 of 13 steps (92%) done Select jobs to execute...

[Wed Oct 30 17:38:39 2024] localrule all: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz.md5 jobid: 0 reason: Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/outs/visualization.tar.gz.md5 resources: tmpdir=/tmp

[Wed Oct 30 17:38:39 2024] Finished job 0. 13 of 13 steps (100%) done Complete log: .snakemake/log/2024-10-30T142338.845878.snakemake.log

STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register: I do not have it

Clouate commented 3 weeks ago

@laomaizi-beagle Thank you, the above log seems to be the log about saw count log? I also want the log about saw realign .What is the content of STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE of saw realign?

laomaizi-beagle commented 3 weeks ago

sorry,for that! I made a mistake ,after adjusting the image ,I run a SAW count but not realign ! I am deeply sorry for that but the second time of count pipeline also showed I failed my image QC

Clouate commented 3 weeks ago

I see, could you use the new tar.gz output from StereoMap-ImageProcessing to run saw realign?

laomaizi-beagle commented 3 weeks ago

thank you very much ,I will run saw realign ,thank you very much!!!!!! I will paste the result log to here as I finished it

laomaizi-beagle commented 3 weeks ago

pipelines-log/log: Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Job stats: job count

all 1 cellcut 1 register 1 report 1 saturation 1 spatialcluster 1 tissuecut 1 tissuecut_micro 1 visualization 1 total 9

Select jobs to execute...

[Thu Oct 31 14:45:57 2024] rule register: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register jobid: 3 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/performance_register reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag threads: 8 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/register/register/main.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/image/D03254G212_SC_20241030_141229_4.0.1.tar.gz -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE --sn D03254G212 -v /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212.raw.gef --gpu -1 --core 8 -w True >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register 2>&1 [Thu Oct 31 14:46:05 2024] Finished job 3. 1 of 9 steps (11%) done Select jobs to execute...

[Thu Oct 31 14:46:05 2024] rule tissuecut: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/lasso_mask.flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut jobid: 2 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_tissuecut reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/lasso_mask.flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag threads: 8 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212.merge.barcodeReadsCount.txt --sn D03254G212 -O Transcriptomics -d -t 8 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 /share/home/lvbin/SAW_soft/saw-8.0.2/lib/geftools/bin/geftools bgef -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.qcfail.gef -O Transcriptomics -b 1,5,10,20,50,100,150,200 -t 1 >>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 [Thu Oct 31 14:46:59 2024] Finished job 2. 2 of 9 steps (22%) done Select jobs to execute...

[Thu Oct 31 14:47:00 2024] rule tissuecut_micro: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/micro_flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/lasso_mask.flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut_micro jobid: 8 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_tissuecut_micro reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/lasso_mask.flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef threads: 8 resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... [Thu Oct 31 14:47:02 2024] Finished job 8. 3 of 9 steps (33%) done Select jobs to execute...

[Thu Oct 31 14:47:02 2024] rule spatialcluster: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/log_spatialcluster jobid: 6 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/performance_spatialcluster reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef resources: tmpdir=/tmp

[Thu Oct 31 14:47:02 2024] rule saturation: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_saturation jobid: 7 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/performance_saturation reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef resources: tmpdir=/tmp

[Thu Oct 31 14:47:02 2024] rule cellcut: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_cellcut jobid: 4 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_cellcut reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_spatialcluster/spatial_cluster.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -s 200 -r 1.0 -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/log_spatialcluster 2>&1 /share/home/lvbin/SAW_soft/saw-8.0.2/lib/saw_saturation/saturation -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212_raw_barcode_gene_exp.txt --tissue /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT --bcstat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat --summary /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_saturation 2>&1 [Thu Oct 31 14:47:03 2024] Finished job 4. 4 of 9 steps (44%) done [Thu Oct 31 14:47:11 2024] Finished job 7. 5 of 9 steps (56%) done [Thu Oct 31 14:47:44 2024] Finished job 6. 6 of 9 steps (67%) done Select jobs to execute...

[Thu Oct 31 14:47:44 2024] rule report: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Log.final.out, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_report jobid: 5 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/performance_report reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut_micro_flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... python /share/home/lvbin/SAW_soft/saw-8.0.2/lib/report_v3/v4/main.pyc -m /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.CIDMap.stat,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.CIDMap.stat -a /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Log.final.out,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Log.final.out -g /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat -l /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat -n /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef -d /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/D03254G212.bin200_1.0.h5ad -t /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/saturation.json -b /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_200x200_MID_gene_counts.png -v /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_200x200_MID_gene.png -c /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_200x200_MID_gene_DNB.png --bin20violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_20x20_MID_gene.png --bin20MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_20x20_MID_gene_DNB.png --bin20Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_20x20_MID_gene_counts.png --bin50violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_50x50_MID_gene.png --bin50MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_50x50_MID_gene_DNB.png --bin50Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_50x50_MID_gene_counts.png --bin100violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_100x100_MID_gene.png --bin100MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_100x100_MID_gene_DNB.png --bin100Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_100x100_MID_gene_counts.png --bin150violin /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/violin_150x150_MID_gene.png --bin150MIDGeneDNB /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/statistic_150x150_MID_gene_DNB.png --bin150Saturation /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig/scatter_150x150_MID_gene_counts.png --pipelineVersion 8.0.2 -s Toad_Gland_re1 --species toad --tissue gland --reference toad -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT --qc_metrics /share/home/lvbin/SAW_soft/saw-8.0.2/config/Metrics_default.xlsx --squareBinMarker /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANALYSIS/bin200_marker_features.csv >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/log_report 2>&1 [Thu Oct 31 14:47:49 2024] Finished job 5. 7 of 9 steps (78%) done Select jobs to execute...

[Thu Oct 31 14:47:49 2024] rule visualization: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/outs/visualization.tar.gz jobid: 1 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/performance_visulization reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/outs/visualization.tar.gz; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/REPORT/AnalysisReport/report.html, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef resources: tmpdir=/tmp

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 8 Rules claiming more threads will be scaled down. Select jobs to execute... [Thu Oct 31 14:48:30 2024] Finished job 1. 8 of 9 steps (89%) done Select jobs to execute...

[Thu Oct 31 14:48:30 2024] localrule all: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/outs/visualization.tar.gz jobid: 0 reason: Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/outs/visualization.tar.gz resources: tmpdir=/tmp

[Thu Oct 31 14:48:30 2024] Finished job 0. 9 of 9 steps (100%) done Complete log: .snakemake/log/2024-10-31T144555.840738.snakemake.log

STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register: [INFO 20241031-14-46-02 p3377897 check_image main.py:80] Verify image data /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/image/D03254G212_SC_20241030_141229_4.0.1.tar.gz file for registration [INFO 20241031-14-46-02 p3377897 check_image main.py:82] Image verification successful. [INFO 20241031-14-46-02 p3377897 create_auto_manual_attrs main.py:216] Pipeline need to handle these subtask: ['stitch', 'tissueseg', 'cellseg']. [INFO 20241031-14-46-02 p3377897 run main.py:511] >> Next do the Stitch task. [INFO 20241031-14-46-02 p3377897 get_stitch_info stitch.py:78] Use the ScopeStitch stitching algorithm to calculate the stitching coordinates for stitching. [INFO 20241031-14-46-02 p3377897 stitch stitch.py:191] Large image quality control, skip stitching module. [INFO 20241031-14-46-02 p3377897 run main.py:531] >> Next do the Manual Registration task. [INFO 20241031-14-46-02 p3377897 manual_register init.py:58] Rotate and scale the radiation matrix: [1.88, 2.2900895144055506e-16, 2.302335982397024e-16, -1.87] after manual registration [INFO 20241031-14-46-03 p3377897 manual_register init.py:73] Manually register the width: 11763 and height: 11763 after affine transformation [INFO 20241031-14-46-03 p3377897 run main.py:555] HE performs registration based on manual registration parameters. [INFO 20241031-14-46-03 p3377897 run main.py:576] >> Next do the Tissue cut task. [INFO 20241031-14-46-03 p3377897 deep_method tissuecut.py:59] Initialize for tissue seg Namespace(core=8, func=<class 'main.Pipeline'>, gpu='-1', group=None, input='/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/datasets/image/D03254G212_SC_20241030_141229_4.0.1.tar.gz', output='/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland2/Toad_Gland_re1/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE', protein=None, sn='D03254G212', vis='/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/outs/feature_expression/D03254G212.raw.gef', whether_cell=True) [] [INFO 20241031-14-46-03 p3377897 init tissue_segmentation.py:33] start loading model weight [INFO 20241031-14-46-03 p3377897 _f_load_model onnx_net.py:29] loading weight from /share/home/lvbin/SAW_soft/saw-8.0.2/lib/register/weights/tissueseg_bcdu_H_20240201_tf.onnx [INFO 20241031-14-46-03 p3377897 _f_load_model onnx_net.py:38] onnx work on cpu,threads 8 [INFO 20241031-14-46-03 p3377897 init tissue_segmentation.py:35] end loading model weight [INFO 20241031-14-46-03 p3377897 deep_method tissuecut.py:67] Load weights (tissue-HE: /share/home/lvbin/SAW_soft/saw-8.0.2/lib/register/weights/tissueseg_bcdu_H_20240201_tf.onnx) finished. [INFO 20241031-14-46-03 p3377897 deep_method tissuecut.py:69] Tissue Segmentation Traceback (most recent call last): File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/main.py", line 636, in File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/main.py", line 632, in main File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/main.py", line 329, in init File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/main.py", line 591, in run File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/tissuecut/tissuecut.py", line 170, in tissuecut File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/tissuecut/tissuecut.py", line 44, in tissuecut File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/register/register/tissuecut/tissuecut.py", line 90, in deep_method File "/share/home/lvbin/SAW_soft/saw-8.0.2/anaconda/lib/python3.8/site-packages/cellbin/dnn/tseg/bcdu/processing.py", line 27, in f_prepocess img = img[:, :, 1] IndexError: too many indices for array: array is 2-dimensional, but 3 were indexed

Clouate commented 3 weeks ago

May I confirm that you are using the ssDNA/DAPI staining image (that is, when you open it, it is a grayscale image, not a color image), but you selected the H&E staining type during ImageProcessing?

laomaizi-beagle commented 3 weeks ago

not really, during ImageProcessing I choose ssDNA/DAPI staining

Clouate commented 3 weeks ago

Thanks, but I'm not quite sure what type of stain your image is, I can only infer the situation based on the log...according to the content of log_register '[INFO 20241031-14-46-03 p3377897 run main.py:555] HE performs registration based on manual registration parameters‘. This is a record, which means that the H&E staining type was selected during StereoMap processing. If the image you use is a grayscale ssDNA/DAPI stained image, please select ssDNA/DAPI as the staining type in step 1, as shown in the figure below 1730363699454