2022-05-10 16:59:02 [time] __start__
2022-05-10 16:59:02 [monitor] cgroup memory limit of 9223372036854771712 bytes detected
2022-05-10 16:59:02 [info] Running crconverter: crconverter dimitri-multi SC_RNA_COUNTER_CS --matrix /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix.h5 --analysis /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/analysis/analysis.h5 --output /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/CLOUPE_PREPROCESS/fork_dimitri-multi/chnk0-ucc6a7a7db6/files/output_for_cloupe.cloupe --description  --metrics /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/_SAMPLE_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork_dimitri-multi/join-ucc6a7a7db3/files/summary.json --gemgroups /scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/CLOUPE_PREPROCESS/fork_dimitri-multi/chnk0-ucc6a7a7db6/files/gem_group_index_json.json
2022-05-10 16:59:11 [info] crconverter output: b"inputs: {name:dimitri-multi description: pipestanceType:1 outputPath:/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/CLOUPE_PREPROCESS/fork_dimitri-multi/chnk0-ucc6a7a7db6/files/output_for_cloupe.cloupe matrixPath:/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix.h5 analysisPath:/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/analysis/analysis.h5 metricsPath:/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/_SAMPLE_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork_dimitri-multi/join-ucc6a7a7db3/files/summary.json aggregationPath: gemGroupsPath:/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/CLOUPE_PREPROCESS/fork_dimitri-multi/chnk0-ucc6a7a7db6/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/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-ucc6a7a7d79/files/dimitri-multi_filtered_feature_barcode_matrix.h5\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23294874531584:\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 23294874531584:\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 23294874531584:\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 23294874531584:\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/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork_dimitri-multi/join-ucc6a7a7d8e/files/analysis/analysis.h5\nHDF5-DIAG: Error detected in HDF5 (1.10.6) thread 23294849124096:\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 23294849124096:\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 23294849124096:\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 23294849124096:\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/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/SAMPLE_REPORTER/CLOUPE_PREPROCESS/fork_dimitri-multi/chnk0-ucc6a7a7db6/files/output_for_cloupe.cloupe\n"
2022-05-10 16:59:11 [time] __end__
