[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "main", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/journal/ID.10X_G171B_mm10.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk15.u40122a10e9"] }
/share/pkg.7/cellranger/3.0.1/install/cellranger-cs/3.0.1/lib/bin/cr_stage martian mark_duplicates main /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/journal/ID.10X_G171B_mm10.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk15.u40122a10e9
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "main", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/journal/ID.10X_G171B_mm10.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk15.u40122a10e9", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u40122a10e9/_log", read: false, write: true } }
