2023-05-19 19:17:00 [time] __start__
2023-05-19 19:17:00 [monitor] cgroup memory limit of 107374182400 bytes detected
2023-05-19 19:17:00 [info] Running crconverter: crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json
2023-05-19 19:17:05 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                              229895  231836      10     7         0      48         0       6 /gpfs/share/apps/spaceranger/1.2.1/external/martian/bin/mrjob /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229901     515      91     1         0    3405         0      82   python /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229919  117171    1006     4         0     506         0       2     crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json 
2023-05-19 19:17:05 [monitor] Stage exceeded its address space quota (using 341.3, allowed 9G)
2023-05-19 19:17:10 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                              229895  231836      10     7         0     100         0       8 /gpfs/share/apps/spaceranger/1.2.1/external/martian/bin/mrjob /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229901     515      91     1         0    3405         0      82   python /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229919  117436    1263     4         0     506         0       3     crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json 
2023-05-19 19:17:10 [monitor] Stage exceeded its address space quota (using 341.6, allowed 9G)
2023-05-19 19:17:15 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                              229895  231836      10     7         0     152         0      10 /gpfs/share/apps/spaceranger/1.2.1/external/martian/bin/mrjob /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229901     515      91     1         0    3405         0      82   python /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229919  117436    1260     4         0    3157         0       5     crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json 
2023-05-19 19:17:15 [monitor] Stage exceeded its address space quota (using 341.6, allowed 9G)
2023-05-19 19:17:20 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                              229895  231836      10     7         0     204         0      12 /gpfs/share/apps/spaceranger/1.2.1/external/martian/bin/mrjob /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229901     515      91     1         0    3405         0      82   python /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229919  117436    1255     4         0    4646         0       9     crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json 
2023-05-19 19:17:20 [monitor] Stage exceeded its address space quota (using 341.6, allowed 9G)
2023-05-19 19:17:25 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                              229895  231836      10     7         0     257         0      14 /gpfs/share/apps/spaceranger/1.2.1/external/martian/bin/mrjob /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229901     515      91     1         0    3405         0      82   python /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229919  156002    1253     5         0    7293         0      11     crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json 
2023-05-19 19:17:25 [monitor] Stage exceeded its address space quota (using 379.3, allowed 9G)
2023-05-19 19:17:30 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                              229895  231836      10     7         0     311         0      16 /gpfs/share/apps/spaceranger/1.2.1/external/martian/bin/mrjob /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229901     515      91     1         0    3417         0      82   python /gpfs/share/apps/spaceranger/1.2.1/external/martian/adapters/python/martian_shell.py /gpfs/share/apps/spaceranger/1.2.1/mro/rna/stages/cloupe/cloupe_preprocess main /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ufe8a68036c 
                              229919  156132    1259     5         0    9510         0     111     crconverter ST358_A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 --output /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json --spatial-image-path /gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif --spatial-tissue-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json 
2023-05-19 19:17:30 [monitor] Stage exceeded its address space quota (using 379.4, allowed 9G)
2023-05-19 19:17:34 [info] crconverter output: inputs: {name:ST358_A1 description: pipestanceType:12 outputPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe matrixPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5 analysisPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5 metricsPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json aggregationPath: gemGroupsPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json contigInfoPath: peakLocationsPath: fragmentsIndexPath: geneAnnotationsPath: geneAnnotationTypes:[] spatialImagePath:/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif spatialFiducialsPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt spatialTissuePath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv spatialDziPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json spatialTilesPaths:[/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files] spatialScaleFactorsPath:/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json spatialAggregationPath: spatialImageType:brightfield}
Converting matrix:  /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5
Converting analysis.h5:  /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140656080107264:
  #000: H5D.c line 358 in H5Dopen2(): not found
    major: Dataset
    minor: Object not found
  #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object
    major: Symbol table
    minor: Object not found
  #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'pattern' doesn't exist
    major: Symbol table
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140656080107264:
  #000: H5D.c line 358 in H5Dopen2(): not found
    major: Dataset
    minor: Object not found
  #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object
    major: Symbol table
    minor: Object not found
  #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #004: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'read' doesn't exist
    major: Symbol table
    minor: Object not found
Converting tissue locations into a projection
Converting fiducial locations into a projection
Embedding image tiles:  /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files
Converting RunInfo
Wrote .cloupe file to /gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe

2023-05-19 19:17:34 [time] __end__
