[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/journal/ID.10X_TCPO_premRNA_Transcript.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u025ec225d4"] }
/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/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/journal/ID.10X_TCPO_premRNA_Transcript.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u025ec225d4
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/journal/ID.10X_TCPO_premRNA_Transcript.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u025ec225d4", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Transcript/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u025ec225d4/_log", read: false, write: true } }
[2019-11-05 20:46:00][INFO] Found first block at real offset 2590
[2019-11-05 21:55:14][INFO] Found 2424332 blocks
[2019-11-05 21:55:14][INFO] size_gb=32.579016032, chunk_size_gb=0.5, num_chunks=66
[2019-11-05 21:55:14][INFO] Found first block at real offset 2590
[2019-11-05 21:55:14][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:14][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:15][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:16][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-11-05 21:55:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
