2023-04-17 16:49:55 [time] __start__
2023-04-17 16:49:55 [monitor] cgroup memory limit of 137438953472 bytes detected
2023-04-17 16:49:55 [info] Running crconverter: crconverter 359-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-359/ST-359-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json
2023-04-17 16:50:00 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               61995  231773      10     7         0      63         0       7 /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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62002  308534      91     9         0    3429         0      78   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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62018  348172     725    10         0     239         0      75     crconverter 359-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-359/ST-359-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json 
2023-04-17 16:50:00 [monitor] Stage exceeded its address space quota (using 867.7, allowed 9G)
2023-04-17 16:50:05 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               61995  231774      10     7         0     143         0       9 /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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62002  308534      91     9         0    3462         0      78   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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62018  348236     725    10         0    3692         0     250     crconverter 359-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-359/ST-359-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json 
2023-04-17 16:50:05 [monitor] Stage exceeded its address space quota (using 867.7, allowed 9G)
2023-04-17 16:50:10 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               61995  231774      10     7         0     224         0      11 /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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62002  308534      91     9         0    3465         0      78   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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62018  386803     724    11         0    4956         0     658     crconverter 359-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-359/ST-359-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json 
2023-04-17 16:50:10 [monitor] Stage exceeded its address space quota (using 905.4, allowed 9G)
2023-04-17 16:50:15 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               61995  231774      10     7         0     307         0      13 /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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62002  308534      91     9         0    3465         0      78   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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62018  425306     693    12         0    5696         0    1030     crconverter 359-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-359/ST-359-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json 
2023-04-17 16:50:15 [monitor] Stage exceeded its address space quota (using 943.0, allowed 9G)
2023-04-17 16:50:20 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               61995  231774      10     7         0     391         0      15 /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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62002  308534      91     9         0    3465         0      78   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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3 /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.udc993db0f3 
                               62018  425306     678    12         0    6796         0    1580     crconverter 359-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-359/ST-359-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json 
2023-04-17 16:50:20 [monitor] Stage exceeded its address space quota (using 943.0, allowed 9G)
2023-04-17 16:50:21 [info] crconverter output: inputs: {name:359-A1 description: pipestanceType:12 outputPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe matrixPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5 analysisPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5 metricsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-udc993db0ed/files/metrics_summary_json.json aggregationPath: gemGroupsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/gem_group_index_json.json contigInfoPath: peakLocationsPath: fragmentsIndexPath: geneAnnotationsPath: geneAnnotationTypes:[] spatialImagePath:/gpfs/home/jw7078/ST-359/ST-359-A1.jpg spatialFiducialsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/fiducial_positions_list.txt spatialTissuePath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-udc993dac7e/files/tissue_positions_list.csv spatialDziPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_info.json spatialTilesPaths:[/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files] spatialScaleFactorsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-udc993dac79/files/scalefactors_json.json spatialAggregationPath: spatialImageType:brightfield}
Converting matrix:  /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-udc993db016/files/filtered_matrices_h5.h5
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140494352938752:
  #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 140494352938752:
  #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
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140494352938752:
  #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 'sequence' doesn't exist
    major: Symbol table
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140494352938752:
  #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 'interval' doesn't exist
    major: Symbol table
    minor: Object not found
Converting analysis.h5:  /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udc993db0ea/files/analysis/analysis.h5
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140615707408128:
  #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 140615707408128:
  #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
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140615707408128:
  #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 'sequence' doesn't exist
    major: Symbol table
    minor: Object not found
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140615707408128:
  #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 'interval' 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/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-udc993dac68/files/dzi_tiles_paths/tiles_0_0_files
Converting RunInfo
Wrote .cloupe file to /gpfs/data/yanailab/projects/jw7078/processed_data/359-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-udc993db0f3/files/output_for_cloupe.cloupe

2023-04-17 16:50:21 [time] __end__
