cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o Sig_18_Blood.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 1843.732 CPU sec, 64.222 real sec
[M::process] read 125180 sequences (18146427 bp) in 0.307 CPU sec, 0.311 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44859, 0, 0)
[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: (191, 289, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 863)
[M::mem_pestat] mean and std.dev: (315.14, 156.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1087)
[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 125180 reads in 25.016 CPU sec, 0.837 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: 125180
overall: 68482572288 mem 1710.958 user 164.409 sys 71.754 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_Blood.L003\tPU:L003\tSM:Sig_18_Blood\tLB:Sig_18_Blood\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_Blood_R1.fastq.gz Sig_18_Blood_R2.fastq.gz
[main] Real time: 71.796 sec; CPU: 1875.371 sec
sorting block 0, #reads = 125327 mem = 60250287 peak = 168394752
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: 7480298
output reads: 125327
bam_mem_sort: 1 calls 0.018 user 0.000 sys 0.028 real
bam_write: 1 calls 0.117 user 0.002 sys 0.118 real
execute: 1 calls 0.020 user 0.182 sys 72.236 real
merge_files: 1 calls 0.009 user 0.143 sys 0.278 real
parse_chunk: 2 calls 0.074 user 0.029 sys 0.112 real
read_chunk: 8 calls 0.041 user 0.083 sys 6.503 real
sort_block: 1 calls 0.173 user 0.115 sys 6.558 real
write_chunk: 4 calls 0.000 user 0.032 sys 0.049 real
overall: 483090432 mem 1.269 user 0.448 sys 72.261 real
ls: cannot access '*.cram': No such file or directory