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 2660.943 CPU sec, 93.663 real sec
[M::process] read 125234 sequences (17709222 bp) in 0.176 CPU sec, 0.179 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 47032, 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: (154, 225, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (246.51, 119.92)
[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 125234 reads in 17.113 CPU sec, 0.571 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: 125234
overall: 68287545344 mem 2200.717 user 483.397 sys 100.299 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.L007\tPU:L007\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: 100.331 sec; CPU: 2684.116 sec
sorting block 0, #reads = 125460 mem = 59662775 peak = 163667968
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: 7062537
output reads: 125460
bam_mem_sort: 1 calls 0.019 user 0.000 sys 0.029 real
bam_write: 1 calls 0.083 user 0.012 sys 0.090 real
execute: 1 calls 0.059 user 0.134 sys 100.731 real
merge_files: 1 calls 0.043 user 0.110 sys 0.267 real
parse_chunk: 2 calls 0.065 user 0.022 sys 0.096 real
read_chunk: 8 calls 0.027 user 0.077 sys 6.001 real
sort_block: 1 calls 0.142 user 0.064 sys 6.034 real
write_chunk: 4 calls 0.007 user 0.030 sys 0.054 real
overall: 457035776 mem 1.288 user 0.347 sys 100.750 real
ls: cannot access '*.cram': No such file or directory