[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/journal/ID.10X_G171B_mm10.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u40122a10c9"] }
/share/pkg.7/cellranger/3.0.1/install/cellranger-cs/3.0.1/lib/bin/cr_stage martian mark_duplicates split /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/journal/ID.10X_G171B_mm10.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u40122a10c9
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/journal/ID.10X_G171B_mm10.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u40122a10c9", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u40122a10c9/_log", read: false, write: true } }
[2020-01-23 16:31:54][INFO] Found first block at real offset 2502
[2020-01-23 16:32:09][INFO] Found 2260093 blocks
[2020-01-23 16:32:09][INFO] size_gb=26.037250315, chunk_size_gb=0.5, num_chunks=53
[2020-01-23 16:32:09][INFO] Found first block at real offset 2502
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:09][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:10][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:11][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2020-01-23 16:32:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
