[stderr]
Running 'annotate_reads' 'main' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ALIGN_READS/fork0/chnk08-u025ec1efae/files/genome_output.bam' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/chnk08-u025ec1ee8c/files/tags.fastq.lz4' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk08-u025ec1fe43/files/output.bam' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk08-u025ec1fe43/files/chunked_reporter.bincode' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_v1.0_ensembl_usethis' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk08-u025ec1fe43/files/gene_index_tab' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u025ec1ee86/files/barcode_counts.json' '/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/python/cellranger/barcodes/3M-february-2018.txt.gz' '1' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/chnk08-u025ec1fe43/files/chunk_metadata.json' '+' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u025ec1ee86/files/feature_counts.json' 'Gene Expression' '0' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/split-u025ec1fe3d/files/libraries.json' '--bam-comments' '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/split-u025ec1fe3d/files/bam_comments.json' '--skip-translate'
