[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "main", "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67", "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67/files", "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/journal/ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk16.u85e8944f67"] }
/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/bin/cr_stage martian mark_duplicates main /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67 /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67/files /ufrc/ewang/lancetdenes/libLTD/h2b_run2/journal/ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk16.u85e8944f67
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "main", metadata_path: "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67", files_path: "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67/files", run_file: "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/journal/ID.h2b_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk16.u85e8944f67", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67/_log", read: false, write: true } }
