2023-12-05 01:45:43 [time] __start__
2023-12-05 01:45:43 [monitor] cgroup memory limit of 9223372036854771712 bytes detected
2023-12-05 01:45:44 [info] Running crconverter: crconverter pbmc_granulocyte_sorted_10k SC_ATAC_GEX_COUNTER --matrix /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/loupe_matrix_h5.h5 --analysis /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/analysis_h5.h5 --output /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/output_for_cloupe.cloupe --description "pbmc_granulocyte_sorted_10k" --peaks /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/headerless_peaks.bed --fragmentsindex /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/fragments.tsv.gz.tbi --geneannotations /home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/genes/genes.gtf.gz --contiginfo /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/contig_info.json --metrics /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u3b7f6ec6d4/files/summary.json
2023-12-05 01:56:59 [info] crconverter output: b'inputs: {name:pbmc_granulocyte_sorted_10k description:"pbmc_granulocyte_sorted_10k" pipestanceType:13 outputPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/output_for_cloupe.cloupe matrixPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/loupe_matrix_h5.h5 analysisPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/analysis_h5.h5 metricsPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u3b7f6ec6d4/files/summary.json aggregationPath: gemGroupsPath: contigInfoPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/contig_info.json peakLocationsPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/headerless_peaks.bed fragmentsIndexPath:/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/fragments.tsv.gz.tbi geneAnnotationsPath:/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/genes/genes.gtf.gz geneAnnotationTypes:[] spatialImagePath: spatialFiducialsPath: spatialTissuePath: spatialDziPath: spatialTilesPaths:[] spatialScaleFactorsPath: spatialAggregationPath: spatialImageType: analysisTitle:Default Pipeline Analysis cellsPerTag: cellsPerProtospacer:}\nConverting matrix:  /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/loupe_matrix_h5.h5\nConverting analysis.h5:  /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/analysis_h5.h5\nConverting RunInfo\nConverting peak info:  /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/headerless_peaks.bed\nConverting gene annotations:  /home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/genes/genes.gtf.gz\nConverting transcript annotations:  /home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0/genes/genes.gtf.gz\nConverting fragments index:  /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/fragments.tsv.gz.tbi\nWrote .cloupe file to /home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u3b7f6ec716/files/output_for_cloupe.cloupe\n'
2023-12-05 01:56:59 [time] __end__
