[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/journal/ID.10X_Chow_2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u99f6b336af"] }
/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/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/journal/ID.10X_Chow_2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u99f6b336af
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/journal/ID.10X_Chow_2.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u99f6b336af", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/10X_Chow_2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u99f6b336af/_log", read: false, write: true } }
[2019-10-25 13:53:53][INFO] Found first block at real offset 2503
[2019-10-25 13:54:15][INFO] Found 3372361 blocks
[2019-10-25 13:54:15][INFO] size_gb=41.667976032, chunk_size_gb=0.5, num_chunks=84
[2019-10-25 13:54:15][INFO] Found first block at real offset 2503
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-10-25 13:54:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
