cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_tumor.bam --sam2bam -
This software is licensed to bgold@natera.com by Sentieon Inc.
This software is licensed to bgold@natera.com by Sentieon Inc.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 1356.721 CPU sec, 48.674 real sec
[M::process] read 125626 sequences (18098646 bp) in 0.175 CPU sec, 0.184 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 44052, 2, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (182, 274, 395)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 821)
[M::mem_pestat] mean and std.dev: (299.15, 150.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1034)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 125626 reads in 9.517 CPU sec, 0.321 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125626
overall: 68521902080 mem 1285.087 user 87.852 sys 55.705 real
[main] Version: 0.7.17-r1188
[main] CMD: /opt/conda/share/sentieon-202308.03-3/libexec/bwa mem -K 100000000 -Y -R @RG\tID:REGRESSION.HCC1395_tumor.L002\tPU:L002\tSM:HCC1395_tumor\tLB:HCC1395_tumor\tDS:s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA -t 31 ./BWAIndex/Homo_sapiens_assembly38.fasta.64 HCC1395_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 55.755 sec; CPU: 1372.942 sec
sorting block 0, #reads = 125801 mem = 60183308 peak = 168439808
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 7344186
output reads: 125801
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.024 real
bam_write: 1 calls 0.119 user 0.000 sys 0.121 real
execute: 1 calls 0.043 user 0.153 sys 56.200 real
merge_files: 1 calls 0.043 user 0.108 sys 0.285 real
parse_chunk: 2 calls 0.063 user 0.009 sys 0.084 real
read_chunk: 8 calls 0.054 user 0.018 sys 6.655 real
sort_block: 1 calls 0.202 user 0.020 sys 6.706 real
write_chunk: 4 calls 0.005 user 0.017 sys 0.035 real
overall: 480059392 mem 1.287 user 0.347 sys 56.225 real
ls: cannot access '*.cram': No such file or directory