[stdout]
Martian runtime detected. Try Num. = 1
['crconverter', u'ST358_A1', u'SPATIAL_RNA_COUNTER_CS', '--matrix', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/FILTER_BARCODES/fork0/join-ufe8a68009c/files/filtered_matrices_h5.h5', '--analysis', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-ufe8a680361/files/analysis/analysis.h5', '--output', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/output_for_cloupe.cloupe', '--description', u'', '--metrics', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/SPATIAL_REPORTER/fork0/chnk0-ufe8a680365/files/metrics_summary_json.json', '--spatial-image-path', u'/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/ST-358.svs_0_MAG1.12x_6_ROT0_BOX3273.13014_19757.13014_19757.28497_3273.28497.tif', '--spatial-tissue-path', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/DETECT_TISSUE/fork0/chnk0-ufe8a67f4df/files/tissue_positions_list.csv', '--spatial-dzi-path', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_info.json', '--spatial-tiles-paths', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_TILE_IMAGES/fork0/join-ufe8a67f4d3/files/dzi_tiles_paths/tiles_0_0_files', '--spatial-fiducials-path', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt', '--spatial-scalefactors-path', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json', '--spatial-image-type', 'brightfield', '--gemgroups', u'/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-ufe8a68036c/files/gem_group_index_json.json']
