[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u85e8944f33", "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u85e8944f33/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.u85e8944f33"] }
/apps/cellranger/3.1.0/cellranger-cs/3.1.0/lib/bin/cr_stage martian mark_duplicates split /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u85e8944f33 /ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u85e8944f33/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.u85e8944f33
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u85e8944f33", files_path: "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u85e8944f33/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.u85e8944f33", 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/split-u85e8944f33/_log", read: false, write: true } }
[2019-10-02 03:18:11][INFO] Found first block at real offset 1582
[2019-10-02 03:18:46][INFO] Found 1728047 blocks
[2019-10-02 03:18:46][INFO] size_gb=19.39940587, chunk_size_gb=0.5, num_chunks=39
[2019-10-02 03:18:46][INFO] Found first block at real offset 1582
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-02 03:18:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
