[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/journal/ID.10X_G171C_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u66f171eea9"] }
/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/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/journal/ID.10X_G171C_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u66f171eea9
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/journal/ID.10X_G171C_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u66f171eea9", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u66f171eea9/_log", read: false, write: true } }
[2019-09-06 01:29:15][INFO] Found first block at real offset 2561
[2019-09-06 01:29:28][INFO] Found 1958770 blocks
[2019-09-06 01:29:28][INFO] size_gb=22.580429843, chunk_size_gb=0.5, num_chunks=46
[2019-09-06 01:29:28][INFO] Found first block at real offset 2561
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:28][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 01:29:29][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
