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slurm-16554857.out
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slurm-16554857.out
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/cm/local/apps/slurm/var/spool/job16554857/slurm_script: line 5: __conda_exe: command not found
[bam_sort_core] merging from 6 files and 1 in-memory blocks...
Command being timed: "samtools sort -o /home/ndr/bgmp/bioinfo/Bi624/Deduper/Deduper-nelsonruth11/C1_SE_uniqAlign_sorted.sam /home/ndr/bgmp/bioinfo/Bi624/Deduper/Deduper-nelsonruth11/C1_SE_uniqAlign.sam"
User time (seconds): 39.38
System time (seconds): 2.10
Percent of CPU this job got: 98%
Elapsed (wall clock) time (h:mm:ss or m:ss): 0:42.28
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 933288
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 42762
Voluntary context switches: 5541
Involuntary context switches: 32
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0
Chromosome: 1 Count: 697508
Chromosome: 10 Count: 564903
Chromosome: 11 Count: 1220389
Chromosome: 12 Count: 359951
Chromosome: 13 Count: 467659
Chromosome: 14 Count: 387239
Chromosome: 15 Count: 437465
Chromosome: 16 Count: 360923
Chromosome: 17 Count: 517566
Chromosome: 18 Count: 290506
Chromosome: 19 Count: 571665
Chromosome: 2 Count: 2787018
Chromosome: 3 Count: 547615
Chromosome: 4 Count: 589839
Chromosome: 5 Count: 562160
Chromosome: 6 Count: 510818
Chromosome: 7 Count: 1113183
Chromosome: 8 Count: 576463
Chromosome: 9 Count: 627488
Chromosome: MT Count: 202002
Chromosome: X Count: 317853
Chromosome: Y Count: 2247
Chromosome: JH584299.1 Count: 3
Chromosome: GL456233.2 Count: 656
Chromosome: GL456211.1 Count: 6
Chromosome: GL456221.1 Count: 4
Chromosome: GL456354.1 Count: 1
Chromosome: GL456210.1 Count: 5
Chromosome: GL456212.1 Count: 4
Chromosome: JH584304.1 Count: 294
Chromosome: GL456379.1 Count: 2
Chromosome: GL456367.1 Count: 3
Chromosome: GL456239.1 Count: 1
Chromosome: GL456383.1 Count: 1
Chromosome: MU069435.1 Count: 5450
Chromosome: GL456389.1 Count: 1
Chromosome: GL456370.1 Count: 21
Chromosome: GL456390.1 Count: 1
Chromosome: GL456382.1 Count: 1
Chromosome: GL456396.1 Count: 17
Chromosome: GL456368.1 Count: 3
Chromosome: MU069434.1 Count: 3
Command being timed: "./ruth_deduper.py -f C1_SE_uniqAlign_sorted.sam -o C1_SE_deduped.sam -u STL96.txt"
User time (seconds): 294.25
System time (seconds): 182.72
Percent of CPU this job got: 88%
Elapsed (wall clock) time (h:mm:ss or m:ss): 9:01.21
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 839632
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 1206547
Voluntary context switches: 109236
Involuntary context switches: 14009
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0