[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/journal/ID.Chow_3_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.ue9a9a73c45"] }
/share/pkg.7/cellranger/3.1.0/install/bin/cellranger-cs/3.1.0/lib/bin/cr_stage martian mark_duplicates split /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/journal/ID.Chow_3_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.ue9a9a73c45
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/journal/ID.Chow_3_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.ue9a9a73c45", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ue9a9a73c45/_log", read: false, write: true } }
[2019-10-16 11:50:30][INFO] Found first block at real offset 2523
[2019-10-16 11:50:54][INFO] Found 3721188 blocks
[2019-10-16 11:50:54][INFO] size_gb=33.27898737, chunk_size_gb=0.5, num_chunks=67
[2019-10-16 11:50:54][INFO] Found first block at real offset 2523
[2019-10-16 11:50:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:55][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:55][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:55][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:56][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:57][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:58][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 11:50:59][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
