[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/journal/ID.Nash_3_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u9daea77c3f"] }
/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/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/journal/ID.Nash_3_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u9daea77c3f
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/journal/ID.Nash_3_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u9daea77c3f", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u9daea77c3f/_log", read: false, write: true } }
[2019-10-16 16:23:28][INFO] Found first block at real offset 2523
[2019-10-16 16:23:49][INFO] Found 3258693 blocks
[2019-10-16 16:23:49][INFO] size_gb=33.329680845, chunk_size_gb=0.5, num_chunks=67
[2019-10-16 16:23:49][INFO] Found first block at real offset 2523
[2019-10-16 16:23:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:50][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:51][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:52][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:53][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 16:23:54][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
