[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "join", "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1", "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1/files", "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/journal/ID.tdtomato_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.udfa19437e1"] }
/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/bin/cr_stage martian mark_duplicates join /ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1 /ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1/files /ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/journal/ID.tdtomato_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.udfa19437e1
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "join", metadata_path: "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1", files_path: "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1/files", run_file: "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/journal/ID.tdtomato_run2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.udfa19437e1", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1/_log", read: false, write: true } }
