[stderr]
Running 'annotate_reads' 'main' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk37-udfa193a1a7/files/genome_output.bam' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/chnk37-udfa193a143/files/tags.fastq.lz4' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk37-udfa193d80a/files/output.bam' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk37-udfa193d80a/files/chunked_reporter.bincode' '/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk37-udfa193d80a/files/gene_index_tab' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-udfa193a13b/files/barcode_counts.json' '/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/3M-february-2018.txt.gz' '1' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk37-udfa193d80a/files/chunk_metadata.json' '+' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-udfa193a13b/files/feature_counts.json' 'Gene Expression' '0' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/split-udfa193d804/files/libraries.json' '--bam-comments' '/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/split-udfa193d804/files/bam_comments.json' '--skip-translate'
