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SAW-A40004: IPR "ssDNA/QCInfo" attribute "QCPassFlag" is less than 1. #154

Closed Druidzha closed 1 month ago

Druidzha commented 1 month ago

I got an issue , yesterday ，I got the same issue below,and i put the issue on github, i received a probable solution which need to recorect my image manually, but i run the stereomap and found i need a .stereo type file, but i cannot got the full SAW count output files ,i dont have a .stereo file to fix my image ,:( :( :(

my SAW count result are like this structure: Sep 27 21:17 ALIGNMENT Sep 27 21:17 ANNOTATION Sep 27 21:17 EXPRESSION_MATRIX Sep 27 21:17 IMAGE

and i browse the SAW guideline ,found we have not the properly output filefolders.

error code:SAW-A40004: IPR "ssDNA/QCInfo" attribute "QCPassFlag" is less than 1. log_tissuecut:Error in rule tissuecut: jobid: 0 input: /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag output: /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/D03254G212.tissue.gef, /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissue_fig log: /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut (check log file(s) for error details)

SystemExit in file /share/home/lvbin/software/saw-8.0.2/config/base.smk, line 416: Exit Snakemake program: The command Error: python /share/home/lvbin/software/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/1/1/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt --sn D03254G212 -O Transcriptomics -d -t 10 >/share/home/1/1g/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 failed to execute. Error message: File "/share/home/1/software/saw-8.0.2/anaconda/lib/python3.8/concurrent/futures/thread.py", line 57, in run File "/share/home/1/software/saw-8.0.2/config/base.smk", line 416, in __rule_tissuecut File "/share/home/1/software/saw-8.0.2/config/util.py", line 23, in run_command Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-27T221455.731515.snakemake.log

What can i do to solve this issue?

Thanks a lot!!!!

Clouate commented 1 month ago

Hi, firstly, you need to run the saw count without the parameter '--image-tar'. If it goes well, visualization.tar.gz will be output in the outs directory. Download it to your Windows system and unzip it. You could see the .stereo file. Make sure it is placed in the same directory as the other files in the compressed package.

Druidzha commented 1 month ago

thank u veru much for your suggestion ,but my saw count without -- image tar parameter also cant run successful as well.so i can not got a .stereo file either 😭😭😭

---- Replied Message ---- | From | @.> | | Date | 09/28/2024 15:02 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [STOmics/SAW] SAW-A40004: IPR "ssDNA/QCInfo" attribute "QCPassFlag" is less than 1. (Issue #154) |

Hi, firstly, you need to run the saw count without the parameter '--image-tar'. If it goes well, visualization.tar.gz will be output in the outs directory. Download it to your Windows system and unzip it. You could see the .stereo file. Make sure it is placed in the same directory as the other files in the compressed package.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Druidzha commented 1 month ago

thank u veru much for your suggestion ,but my saw count without -- image tar parameter also cant run successful as well.so i can not got a .stereo file either 😭😭😭 … ---- Replied Message ---- | From | @.> | | Date | 09/28/2024 15:02 | | To | @.> | | Cc | @.>@.> | | Subject | Re: [STOmics/SAW] SAW-A40004: IPR "ssDNA/QCInfo" attribute "QCPassFlag" is less than 1. (Issue #154) | Hi, firstly, you need to run the saw count without the parameter '--image-tar'. If it goes well, visualization.tar.gz will be output in the outs directory. Download it to your Windows system and unzip it. You could see the .stereo file. Make sure it is placed in the same directory as the other files in the compressed package. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Druidzha commented 1 month ago

thank u veru much for your suggestion ,but my saw count without -- image tar parameter also cant run successful as well.so i can not got a .stereo file either 😭😭😭 …

Clouate commented 1 month ago

Okay, it would be helpful if you could provide pipelineslogs/log and all the files starting with log under STEREO_ANALYSIS_WORKFLOW_PROCESSING.

Druidzha commented 1 month ago

okok

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...

[Fri Sep 27 18:17:06 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_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/08.D03254G212.Q4.bcPara, /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/13.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/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt, /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/08.D03254G212.Q4.barcodeReadsCount.txt, /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/15.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/04.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt, /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/06.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/03.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt, /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/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.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.barcodeReadsCount.txt, /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/09.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.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt, /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/01.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.CIDMap.stat, /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/09.D03254G212.Q4.bcPara, /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/13.D03254G212.Q4.bcPara, /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/04.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/04.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara, /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/02.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara, /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/14.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/splitBin -t 24 -s 2 -p 2_25 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map 2>&1 /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/saw-8.0.2/lib/saw_cidcount/calBcNumFromMask -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/CIDCount 2>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map /share/home/lvbin/software/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4. --stParaFile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.bcPara >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.run.log 2>>/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_map [Fri Sep 27 19:50:34 2024] Finished job 4. 1 of 13 steps (8%) done Select jobs to execute...

[Fri Sep 27 19:50:35 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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.bcPara output: /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 log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/log_anno jobid: 6 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/performance_anno reason: Missing output files: /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; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.bcPara, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.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/software/saw-8.0.2/lib/saw_count/Bam2Gem -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.Aligned.sortedByCoord.out.bam,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.Aligned.sortedByCoord.out.bam -o /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 -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_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef --sat_file /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/log_anno 2>&1 [Fri Sep 27 21:17:24 2024] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute...

[Fri Sep 27 21:17:25 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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/log_register jobid: 5 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/performance_register reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag; Input files updated by another job: /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 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... [Fri Sep 27 21:17:39 2024] Finished job 5. 3 of 13 steps (23%) done Select jobs to execute...

[Fri Sep 27 21:17:39 2024] rule micro: 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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/micro_flag log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_micro jobid: 12 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_micro reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat threads: 10 resources: tmpdir=/tmp

[Fri Sep 27 21:17:39 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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_merge jobid: 3 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/performance_merge reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/16.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.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/software/saw-8.0.2/lib/saw_merge/mergeBcCount -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/01.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/02.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/03.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/04.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/05.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/06.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/07.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/08.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/09.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/10.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/11.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/12.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/13.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/14.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/15.D03254G212.Q4.barcodeReadsCount.txt,/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt -t 10 >/share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/log_merge 2>&1 [Fri Sep 27 21:17:41 2024] Finished job 12. 4 of 13 steps (31%) done [Fri Sep 27 21:17:44 2024] Finished job 3. 5 of 13 steps (38%) done Select jobs to execute...

[Fri Sep 27 21:17:44 2024] rule tissuecut: input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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/EXPRESSION_MATRIX/tissue_fig log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut jobid: 2 benchmark: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/performance_tissuecut reason: Missing output files: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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/EXPRESSION_MATRIX/tissuecut.stat; Input files updated by another job: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.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... python /share/home/lvbin/software/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 [Fri Sep 27 21:17:51 2024] Error in rule tissuecut: jobid: 0 input: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/IMAGE/flag output: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/tissuecut.stat, /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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/EXPRESSION_MATRIX/tissue_fig log: /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut (check log file(s) for error details)

SystemExit in file /share/home/lvbin/software/saw-8.0.2/config/base.smk, line 416: Exit Snakemake program: The command Error: python /share/home/lvbin/software/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/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_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut 2>&1 failed to execute. Error message: File "/share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/concurrent/futures/thread.py", line 57, in run File "/share/home/lvbin/software/saw-8.0.2/config/base.smk", line 416, in __rule_tissuecut File "/share/home/lvbin/software/saw-8.0.2/config/util.py", line 23, in run_command Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-27T181705.610512.snakemake.log

Clouate commented 1 month ago

What is the content of /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut? If it is empty, would you mind try to run the following code and show the output content?

export LD_LIBRARY_PATH=" /share/home/lvbin/software/saw-8.0.2/anaconda/lib:$LD_LIBRARY_PATH"
 /share/home/lvbin/software/saw-8.0.2/anaconda/bin/python /share/home/lvbin/software/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt --sn D03254G212 -O Transcriptomics -d -t 10
Druidzha commented 1 month ago

ok！let me try！

---- Replied Message ---- | From | @.> | | Date | 09/28/2024 15:44 | | To | @.> | | Cc | @.>、State @.> | | Subject | Re: [STOmics/SAW] SAW-A40004: IPR "ssDNA/QCInfo" attribute "QCPassFlag" is less than 1. (Issue #154) |

What is the content of /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX/log_tissuecut? If it is empty, would you mind try to run the following code and show the output content?

export LD_LIBRARY_PATH=" /share/home/lvbin/software/saw-8.0.2/anaconda/lib:$LD_LIBRARY_PATH" /share/home/lvbin/software/saw-8.0.2/anaconda/bin/python /share/home/lvbin/software/saw-8.0.2/lib/saw_tissuecut/Tissuecut.pyc -i /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ANNOTATION/D03254G212.raw.gef -o /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/EXPRESSION_MATRIX --dnbfile /share/home/lvbin/druidzhang/raw_data/stereo_seq/saw/run/Toad_Gland/STEREO_ANALYSIS_WORKFLOW_PROCESSING/ALIGNMENT/D03254G212.merge.barcodeReadsCount.txt --sn D03254G212 -O Transcriptomics -d -t 10

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Druidzha commented 1 month ago

Loading libts.so time used: 0.401 createBinImg time used: 1.673 readbgef start [2024-09-27 21:17:48] raw gef minx:0 miny:0 maxx:11762 maxy:11762 [2024-09-27 21:17:48] raw gef gene:21293 geneexp:5696824 readbgef - elapsed time: 209.05447 ms createBinImg start createBinImg calc data elapsed time: 101.27575 ms createBinImg - elapsed time: 1672.92156 ms Traceback (most recent call last): File "/share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/python/pywrap_tensorflow.py", line 64, in from tensorflow.python._pywrap_tensorflow_internal import * ImportError: /share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so: ELF load command past end of file

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/Tissuecut.py", line 261, in File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/Tissuecut.py", line 257, in main File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/Tissuecut.py", line 213, in tslib File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/Tissuecut.py", line 22, in newtissue File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/tissuecut/tissuecut_api.py", line 1, in File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/tissuecut/bcdu/bcdu_net.py", line 1, in File "/data/users/zhanhaojia/repo/auto_build/build/saw8.0.2/bin_bk/saw_tissuecut/tissuecut/bcdu/bcdu_model.py", line 2, in File "/share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/init.py", line 41, in from tensorflow.python.tools import module_util as _module_util File "/share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/python/init.py", line 40, in from tensorflow.python import pywrap_tensorflow as _pywrap_tensorflow File "/share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/python/pywrap_tensorflow.py", line 79, in raise ImportError( ImportError: Traceback (most recent call last): File "/share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/python/pywrap_tensorflow.py", line 64, in from tensorflow.python._pywrap_tensorflow_internal import * ImportError: /share/home/lvbin/software/saw-8.0.2/anaconda/lib/python3.8/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so: ELF load command past end of file

Failed to load the native TensorFlow runtime. See https://www.tensorflow.org/install/errors for some common causes and solutions. If you need help, create an issue at https://github.com/tensorflow/tensorflow/issues and include the entire stack trace above this error message. this is my log_tissuecut it is not empty

Clouate commented 1 month ago

The reason may be that SAW conflicts with your running environment, or the SAW software package is incomplete. Consider creating a new empty conda environment first, or re-download SAW and unzip it.

Druidzha commented 1 month ago

Thank you very much ,and i will have a try