[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/journal/ID.10X_G171B_mm9_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u68b572fdc9"] }
/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_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/journal/ID.10X_G171B_mm9_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u68b572fdc9
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/journal/ID.10X_G171B_mm9_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u68b572fdc9", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u68b572fdc9/_log", read: false, write: true } }
[2019-09-06 20:46:03][INFO] Found first block at real offset 1904
[2019-09-06 20:46:17][INFO] Found 2305973 blocks
[2019-09-06 20:46:17][INFO] size_gb=26.272895072, chunk_size_gb=0.5, num_chunks=53
[2019-09-06 20:46:17][INFO] Found first block at real offset 1904
[2019-09-06 20:46:17][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:18][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:19][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-06 20:46:20][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
