[stderr]
Running 'annotate_reads' 'main' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk13-u8c0aa70da9/files/genome_output.bam' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/chnk13-u8c0aa70d28/files/tags.fastq.lz4' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk13-u8c0aa715bb/files/output.bam' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk13-u8c0aa715bb/files/chunked_reporter.bincode' '/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk13-u8c0aa715bb/files/gene_index_tab' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u8c0aa70d24/files/barcode_counts.json' '/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/737K-august-2016.txt' '1' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk13-u8c0aa715bb/files/chunk_metadata.json' '+' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u8c0aa70d24/files/feature_counts.json' 'Gene Expression' '0' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/split-u8c0aa715b4/files/libraries.json' '--bam-comments' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/split-u8c0aa715b4/files/bam_comments.json' '--skip-translate'
