2019-09-19 20:54:38 [time] __start__
2019-09-19 20:54:39 [monitor] cgroup memory limit of 9223372036854771712 bytes detected
2019-09-19 20:54:40 [info] Running crconverter: crconverter 10X_G171B_pcg_only_UseThis SC_RNA_COUNTER_CS --matrix /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u6c19841f2f/files/filtered_matrices_h5.h5 --analysis /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u6c19842216/files/analysis/analysis.h5 --output /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u6c1984234d/files/output_for_cloupe.cloupe --description  --metrics /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/chnk0-u6c19842330/files/metrics_summary_json.json --gemgroups /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u6c1984234d/files/gem_group_index_json.json
2019-09-19 20:54:48 [info] crconverter output: inputs: {name:10X_G171B_pcg_only_UseThis description: pipestanceType:1 outputPath:/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u6c1984234d/files/output_for_cloupe.cloupe matrixPath:/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u6c19841f2f/files/filtered_matrices_h5.h5 analysisPath:/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u6c19842216/files/analysis/analysis.h5 metricsPath:/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/chnk0-u6c19842330/files/metrics_summary_json.json aggregationPath: gemGroupsPath:/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u6c1984234d/files/gem_group_index_json.json contigInfoPath: peakLocationsPath: fragmentsIndexPath: geneAnnotationsPath: geneAnnotationTypes:[]}
Converting matrix:  /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u6c19841f2f/files/filtered_matrices_h5.h5
Converting analysis.h5:  /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u6c19842216/files/analysis/analysis.h5
Converting RunInfo
Wrote .cloupe file to /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u6c1984234d/files/output_for_cloupe.cloupe

2019-09-19 20:54:49 [time] __end__
