2023-07-04 13:39:16 [time] __start__
2023-07-04 13:39:17 [info] Running crconverter: crconverter Nodule_2_gex_only SC_RNA_COUNTER_CS --matrix /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ua092a4739d/files/filtered_matrices_h5.h5 --analysis /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ua092a4754b/files/analysis/analysis.h5 --output /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ua092a47564/files/output_for_cloupe.cloupe --description  --metrics /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ua092a4755e/files/metrics_summary_json.json --gemgroups /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ua092a47564/files/gem_group_index_json.json
2023-07-04 13:39:37 [info] crconverter output: b"inputs: {name:Nodule_2_gex_only description: pipestanceType:1 outputPath:/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ua092a47564/files/output_for_cloupe.cloupe matrixPath:/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ua092a4739d/files/filtered_matrices_h5.h5 analysisPath:/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ua092a4754b/files/analysis/analysis.h5 metricsPath:/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/chnk0-ua092a4755e/files/metrics_summary_json.json aggregationPath: gemGroupsPath:/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ua092a47564/files/gem_group_index_json.json contigInfoPath: peakLocationsPath: fragmentsIndexPath: geneAnnotationsPath: geneAnnotationTypes:[] spatialImagePath: spatialFiducialsPath: spatialTissuePath: spatialDZIPath: spatialTilesPaths:[] spatialScaleFactorsPath: spatialAggregationPath: spatialImageType: spatialEnrichment: spatialImagePageNames:[] analysisTitle:Default Pipeline Analysis cellsPerSample: cellsPerTag: cellsPerProtospacer:}\nConverting matrix:  /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ua092a4739d/files/filtered_matrices_h5.h5\nConverting analysis.h5:  /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ua092a4754b/files/analysis/analysis.h5\nHDF5-DIAG: Error detected in HDF5 (1.12.1) thread 1:\n  #000: H5D.c line 285 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #002: H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #003: H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #004: H5Dint.c line 1483 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #005: H5Gloc.c line 442 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #006: H5Gtraverse.c line 837 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #007: H5Gtraverse.c line 613 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #008: H5Gloc.c line 399 in H5G__loc_find_cb(): object 'secondary_name' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.12.1) thread 1:\n  #000: H5D.c line 285 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #002: H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #003: H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #004: H5Dint.c line 1483 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #005: H5Gloc.c line 442 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #006: H5Gtraverse.c line 837 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #007: H5Gtraverse.c line 613 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #008: H5Gloc.c line 399 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 (1.12.1) thread 1:\n  #000: H5D.c line 285 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #002: H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #003: H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #004: H5Dint.c line 1483 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #005: H5Gloc.c line 442 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #006: H5Gtraverse.c line 837 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #007: H5Gtraverse.c line 613 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #008: H5Gloc.c line 399 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 (1.12.1) thread 1:\n  #000: H5D.c line 285 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #002: H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #003: H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #004: H5Dint.c line 1483 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #005: H5Gloc.c line 442 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #006: H5Gtraverse.c line 837 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #007: H5Gtraverse.c line 613 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #008: H5Gloc.c line 399 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 (1.12.1) thread 1:\n  #000: H5D.c line 285 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #002: H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #003: H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #004: H5Dint.c line 1483 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #005: H5Gloc.c line 442 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #006: H5Gtraverse.c line 837 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #007: H5Gtraverse.c line 613 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #008: H5Gloc.c line 399 in H5G__loc_find_cb(): object 'interval' doesn't exist\n    major: Symbol table\n    minor: Object not found\nHDF5-DIAG: Error detected in HDF5 (1.12.1) thread 1:\n  #000: H5D.c line 285 in H5Dopen2(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #001: H5VLcallback.c line 1910 in H5VL_dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #002: H5VLcallback.c line 1877 in H5VL__dataset_open(): dataset open failed\n    major: Virtual Object Layer\n    minor: Can't open object\n  #003: H5VLnative_dataset.c line 123 in H5VL__native_dataset_open(): unable to open dataset\n    major: Dataset\n    minor: Can't open object\n  #004: H5Dint.c line 1483 in H5D__open_name(): not found\n    major: Dataset\n    minor: Object not found\n  #005: H5Gloc.c line 442 in H5G_loc_find(): can't find object\n    major: Symbol table\n    minor: Object not found\n  #006: H5Gtraverse.c line 837 in H5G_traverse(): internal path traversal failed\n    major: Symbol table\n    minor: Object not found\n  #007: H5Gtraverse.c line 613 in H5G__traverse_real(): traversal operator failed\n    major: Symbol table\n    minor: Callback failed\n  #008: H5Gloc.c line 399 in H5G__loc_find_cb(): object 'isotype_control' doesn't exist\n    major: Symbol table\n    minor: Object not found\nConverting RunInfo\nWrote .cloupe file to /data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/chnk0-ua092a47564/files/output_for_cloupe.cloupe\n"
2023-07-04 13:39:37 [time] __end__
