[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/journal/ID.Nash_2_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u0fe2a74878"] }
/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/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/journal/ID.Nash_2_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u0fe2a74878
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/journal/ID.Nash_2_run.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u0fe2a74878", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u0fe2a74878/_log", read: false, write: true } }
[2019-10-16 12:42:33][INFO] Found first block at real offset 2502
[2019-10-16 12:42:45][INFO] Found 1689071 blocks
[2019-10-16 12:42:45][INFO] size_gb=23.582402997, chunk_size_gb=0.5, num_chunks=48
[2019-10-16 12:42:45][INFO] Found first block at real offset 2502
[2019-10-16 12:42:45][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:45][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:45][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:45][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:45][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:48][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-16 12:42:49][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
