[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/journal/ID.10X_G171C_mm9_default.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.ubcfb745611"] }
/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_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/journal/ID.10X_G171C_mm9_default.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.ubcfb745611
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/journal/ID.10X_G171C_mm9_default.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.ubcfb745611", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-ubcfb745611/_log", read: false, write: true } }
[2019-09-07 21:14:59][INFO] Found first block at real offset 1903
[2019-09-07 21:15:12][INFO] Found 1986186 blocks
[2019-09-07 21:15:12][INFO] size_gb=22.724233559, chunk_size_gb=0.5, num_chunks=46
[2019-09-07 21:15:12][INFO] Found first block at real offset 1903
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:12][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:13][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-07 21:15:14][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
