2022-04-19 17:37:10 [time] __start__
2022-04-19 17:37:10 [monitor] cgroup memory limit of 9223372036854771712 bytes detected
2022-04-19 17:37:10 [info] Running crconverter: crconverter dimitri_RNA_only SC_RNA_COUNTER_CS --matrix /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufc475ed619/files/filtered_matrices_h5.h5 --analysis /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufc475ed6c0/files/analysis/analysis.h5 --output /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ufc475ed726/files/output_for_cloupe.cloupe --description  --metrics /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ufc475ed722/files/metrics_summary_json.json --gemgroups /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ufc475ed726/files/gem_group_index_json.json
2022-04-19 17:37:19 [info] crconverter output: b"inputs: {name:dimitri_RNA_only description: pipestanceType:1 outputPath:/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ufc475ed726/files/output_for_cloupe.cloupe matrixPath:/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufc475ed619/files/filtered_matrices_h5.h5 analysisPath:/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufc475ed6c0/files/analysis/analysis.h5 metricsPath:/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ufc475ed722/files/metrics_summary_json.json aggregationPath: gemGroupsPath:/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ufc475ed726/files/gem_group_index_json.json contigInfoPath: peakLocationsPath: fragmentsIndexPath: geneAnnotationsPath: geneAnnotationTypes:[] spatialImagePath: spatialFiducialsPath: spatialTissuePath: spatialDziPath: spatialTilesPaths:[] spatialScaleFactorsPath: spatialAggregationPath: spatialImageType: spatialEnrichment: analysisTitle:Default Pipeline Analysis cellsPerTag: cellsPerProtospacer:}\nConverting matrix:  /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufc475ed619/files/filtered_matrices_h5.h5\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23435003356928:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'pattern' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23435003356928:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'read' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23435003356928:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'sequence' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23435003356928:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'interval' doesn't exist\n    major: Symbol table\n    minor: Object not found\nConverting analysis.h5:  /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufc475ed6c0/files/analysis/analysis.h5\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23434985240320:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'pattern' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23434985240320:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'read' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23434985240320:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'sequence' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23434985240320:\n  #000: H5D.c line 298 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5Dint.c line 1410 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #002: H5Gloc.c line 422 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'interval' doesn't exist\n    major: Symbol table\n    minor: Object not found\nConverting RunInfo\nWrote .cloupe file to /scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ufc475ed726/files/output_for_cloupe.cloupe\n"
2022-04-19 17:37:19 [time] __end__
