[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-udfa19437e1", "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-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 split /ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-udfa19437e1 /ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-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: "split", metadata_path: "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-udfa19437e1", files_path: "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-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/split-udfa19437e1/_log", read: false, write: true } }
[2019-10-02 01:38:42][INFO] Found first block at real offset 1585
[2019-10-02 01:39:25][INFO] Found 2054274 blocks
[2019-10-02 01:39:25][INFO] size_gb=25.367389926, chunk_size_gb=0.5, num_chunks=51
[2019-10-02 01:39:25][INFO] Found first block at real offset 1585
[2019-10-02 01:39:25][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:25][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:26][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:27][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:27][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:27][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:30][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:30][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:30][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:30][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:31][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:31][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:31][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:31][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:32][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:32][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:32][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:32][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:33][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:33][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:33][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:34][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 01:39:34][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
