cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o Sig_18_tissue.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 1441.901 CPU sec, 50.362 real sec
[M::process] read 125244 sequences (17742351 bp) in 0.162 CPU sec, 0.169 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 46956, 0, 1)
[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: (155, 223, 319)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 647)
[M::mem_pestat] mean and std.dev: (246.06, 119.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 811)
[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 125244 reads in 9.821 CPU sec, 0.338 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: 125244
overall: 68526624768 mem 1350.299 user 107.572 sys 56.855 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.Sig_18_tissue.L002\tPU:L002\tSM:Sig_18_tissue\tLB:Sig_18_tissue\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 Sig_18_tissue_R1.fastq.gz Sig_18_tissue_R2.fastq.gz
[main] Real time: 56.914 sec; CPU: 1457.874 sec
sorting block 0, #reads = 125469 mem = 59623350 peak = 166821888
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: 7030812
output reads: 125469
bam_mem_sort: 1 calls 0.020 user 0.000 sys 0.026 real
bam_write: 1 calls 0.103 user 0.011 sys 0.111 real
execute: 1 calls 0.074 user 0.115 sys 57.295 real
merge_files: 1 calls 0.058 user 0.089 sys 0.265 real
parse_chunk: 2 calls 0.049 user 0.009 sys 0.074 real
read_chunk: 8 calls 0.033 user 0.049 sys 6.108 real
sort_block: 1 calls 0.154 user 0.058 sys 6.154 real
write_chunk: 4 calls 0.011 user 0.016 sys 0.047 real
overall: 482947072 mem 1.228 user 0.297 sys 57.350 real
ls: cannot access '*.cram': No such file or directory