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 2023.184 CPU sec, 71.670 real sec
[M::process] read 124960 sequences (17676029 bp) in 0.171 CPU sec, 0.176 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 46672, 3, 3)
[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, 223, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (246.09, 119.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 818)
[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 124960 reads in 25.870 CPU sec, 0.870 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: 124960
overall: 68388163584 mem 1741.516 user 316.818 sys 81.827 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.L006\tPU:L006\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: 81.862 sec; CPU: 2058.337 sec
sorting block 0, #reads = 125203 mem = 59559176 peak = 160432128
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: 7072948
output reads: 125203
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.026 real
bam_write: 1 calls 0.087 user 0.023 sys 0.109 real
execute: 1 calls 0.098 user 0.107 sys 82.296 real
merge_files: 1 calls 0.079 user 0.077 sys 0.273 real
parse_chunk: 2 calls 0.045 user 0.030 sys 0.082 real
read_chunk: 8 calls 0.039 user 0.044 sys 9.226 real
sort_block: 1 calls 0.157 user 0.070 sys 9.280 real
write_chunk: 4 calls 0.018 user 0.008 sys 0.045 real
overall: 452149248 mem 1.221 user 0.332 sys 82.318 real
ls: cannot access '*.cram': No such file or directory