2023-04-17 16:58:28 [time] __start__
2023-04-17 16:58:28 [monitor] cgroup memory limit of 137438953472 bytes detected
2023-04-17 16:58:29 [info] Running crconverter: crconverter 399-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-399/ST-399-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json
2023-04-17 16:58:33 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               65533  270340      12     8         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65541  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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65557  348176     808    10         0     281         0      75     crconverter 399-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-399/ST-399-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json 
2023-04-17 16:58:33 [monitor] Stage exceeded its address space quota (using 905.3, allowed 9G)
2023-04-17 16:58:38 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               65533  270340      12     8         0     144         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65541  308534      91     9         0    3464         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65557  348306     915    10         0    4545         0     167     crconverter 399-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-399/ST-399-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json 
2023-04-17 16:58:38 [monitor] Stage exceeded its address space quota (using 905.4, allowed 9G)
2023-04-17 16:58:43 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               65533  270340      12     8         0     225         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65541  308534      91     9         0    3467         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65557  348307     890    10         0    5955         0     439     crconverter 399-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-399/ST-399-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json 
2023-04-17 16:58:43 [monitor] Stage exceeded its address space quota (using 905.4, allowed 9G)
2023-04-17 16:58:48 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               65533  270340      12     8         0     308         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65541  308534      91     9         0    3467         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65557  425375     855    12         0    6671         0     797     crconverter 399-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-399/ST-399-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json 
2023-04-17 16:58:48 [monitor] Stage exceeded its address space quota (using 980.7, allowed 9G)
2023-04-17 16:58:53 [monitor] Process tree:
                                 PID VSZ(mb) RSS(mb) Procs  Read(mb) (calls) Write(mb) (calls) COMMAND
                               65533  270340      12     8         0     394         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65541  308534      91     9         0    3467         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/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4 /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/journal/SPATIAL_RNA_COUNTER_CS.CLOUPE_PREPROCESS.fork0.chnk0.ue5873db2f4 
                               65557  463942     820    13         0    7487         0    1204     crconverter 399-A1 SPATIAL_RNA_COUNTER_CS --matrix /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 --analysis /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 --output /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe --description  --metrics /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json --spatial-image-path /gpfs/home/jw7078/ST-399/ST-399-A1.jpg --spatial-tissue-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv --spatial-dzi-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json --spatial-tiles-paths /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files --spatial-fiducials-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt --spatial-scalefactors-path /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json --spatial-image-type brightfield --gemgroups /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json 
2023-04-17 16:58:53 [monitor] Stage exceeded its address space quota (using 1018.4, allowed 9G)
2023-04-17 16:58:58 [info] crconverter output: inputs: {name:399-A1 description: pipestanceType:12 outputPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe matrixPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.h5 analysisPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.h5 metricsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ue5873db2ef/files/metrics_summary_json.json aggregationPath: gemGroupsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json contigInfoPath: peakLocationsPath: fragmentsIndexPath: geneAnnotationsPath: geneAnnotationTypes:[] spatialImagePath:/gpfs/home/jw7078/ST-399/ST-399-A1.jpg spatialFiducialsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt spatialTissuePath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ue5873dae13/files/tissue_positions_list.csv spatialDziPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_info.json spatialTilesPaths:[/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files] spatialScaleFactorsPath:/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json spatialAggregationPath: spatialImageType:brightfield}
Converting matrix:  /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ue5873db1fb/files/filtered_matrices_h5.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
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 'sequence' 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 'interval' doesn't exist
    major: Symbol table
    minor: Object not found
Converting analysis.h5:  /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ue5873db2eb/files/analysis/analysis.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 tissue locations into a projection
Converting fiducial locations into a projection
Embedding image tiles:  /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ue5873dadfe/files/dzi_tiles_paths/tiles_0_0_files
Converting RunInfo
Wrote .cloupe file to /gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe

2023-04-17 16:58:58 [time] __end__
