[stdout]
Martian runtime detected. Try Num. = 1
['crconverter', u'399-A1', u'SPATIAL_RNA_COUNTER_CS', '--matrix', u'/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', u'/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', u'/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/output_for_cloupe.cloupe', '--description', u'', '--metrics', u'/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', u'/gpfs/home/jw7078/ST-399/ST-399-A1.jpg', '--spatial-tissue-path', u'/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', u'/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', u'/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', u'/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', u'/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', u'/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ue5873db2f4/files/gem_group_index_json.json']
