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 1606.668 CPU sec, 56.710 real sec
[M::process] read 124902 sequences (17673402 bp) in 0.166 CPU sec, 0.174 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 46778, 1, 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, 224, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (245.77, 118.86)
[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 124902 reads in 20.743 CPU sec, 0.698 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: 124902
overall: 68506173440 mem 1488.937 user 144.445 sys 63.390 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.L004\tPU:L004\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: 63.426 sec; CPU: 1633.385 sec
sorting block 0, #reads = 125142 mem = 59607517 peak = 166846464
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 192
algo: util-sort
license: sentieon:util=1
output file size: 7084194
output reads: 125142
bam_mem_sort: 1 calls 0.018 user 0.000 sys 0.025 real
bam_write: 1 calls 0.111 user 0.008 sys 0.114 real
execute: 1 calls 0.058 user 0.107 sys 63.829 real
merge_files: 1 calls 0.038 user 0.089 sys 0.250 real
parse_chunk: 2 calls 0.043 user 0.017 sys 0.070 real
read_chunk: 8 calls 0.027 user 0.040 sys 5.925 real
sort_block: 1 calls 0.160 user 0.050 sys 5.978 real
write_chunk: 4 calls 0.006 user 0.021 sys 0.045 real
overall: 480645120 mem 1.154 user 0.288 sys 63.850 real
ls: cannot access '*.cram': No such file or directory