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 2440.088 CPU sec, 85.702 real sec
[M::process] read 124610 sequences (17629509 bp) in 0.172 CPU sec, 0.172 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 46577, 0, 2)
[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: (154, 224, 319)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 649)
[M::mem_pestat] mean and std.dev: (246.13, 119.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 814)
[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 124610 reads in 25.434 CPU sec, 0.858 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124610
overall: 68300124160 mem 2023.575 user 448.456 sys 93.072 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.L005\tPU:L005\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: 93.111 sec; CPU: 2472.034 sec
sorting block 0, #reads = 124855 mem = 59334865 peak = 163651584
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: util-sort
license: sentieon:util=1
output file size: 7013233
output reads: 124855
bam_mem_sort: 1 calls 0.016 user 0.000 sys 0.024 real
bam_write: 1 calls 0.082 user 0.021 sys 0.099 real
execute: 1 calls 0.069 user 0.117 sys 93.507 real
merge_files: 1 calls 0.053 user 0.094 sys 0.266 real
parse_chunk: 2 calls 0.052 user 0.009 sys 0.067 real
read_chunk: 7 calls 0.020 user 0.048 sys 6.467 real
sort_block: 1 calls 0.134 user 0.064 sys 6.493 real
write_chunk: 3 calls 0.027 user 0.013 sys 0.058 real
overall: 456671232 mem 1.199 user 0.327 sys 93.530 real
ls: cannot access '*.cram': No such file or directory