[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "main", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/journal/ID.10X_TCPO_premRNA_Gene.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk36.u6ddfc30b68"] }
/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/bin/cr_stage martian mark_duplicates main /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/journal/ID.10X_TCPO_premRNA_Gene.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk36.u6ddfc30b68
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "main", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/journal/ID.10X_TCPO_premRNA_Gene.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk36.u6ddfc30b68", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68/_log", read: false, write: true } }
