[stdout]
Args { cmd_martian: true, arg_adapter: ["mark_duplicates", "split", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b/files", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/journal/ID.10X_G171B_pcg_only_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u6c1984138b"] }
/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_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b/files /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/journal/ID.10X_G171B_pcg_only_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u6c1984138b
got metadata: Metadata { stage_name: "mark_duplicates", stage_type: "split", metadata_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b", files_path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b/files", run_file: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/journal/ID.10X_G171B_pcg_only_UseThis.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.u6c1984138b", jobinfo: {}, cache: {}, log_file: File { fd: 3, path: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_pcg_only_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/split-u6c1984138b/_log", read: false, write: true } }
[2019-09-19 19:47:25][INFO] Found first block at real offset 2559
[2019-09-19 19:47:40][INFO] Found 2447576 blocks
[2019-09-19 19:47:40][INFO] size_gb=27.131137179, chunk_size_gb=0.5, num_chunks=55
[2019-09-19 19:47:40][INFO] Found first block at real offset 2559
[2019-09-19 19:47:40][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:40][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:40][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:40][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:40][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:41][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:44][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:46][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
[2019-09-19 19:47:47][WARN] Taking a long time to find a chunk boundary. Check your chunk_bound_key function?
