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 1889.557 CPU sec, 70.975 real sec
[M::process] read 125148 sequences (18140009 bp) in 0.183 CPU sec, 0.185 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 45084, 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, 290, 416)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 866)
[M::mem_pestat] mean and std.dev: (315.67, 157.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1091)
[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 125148 reads in 22.816 CPU sec, 0.781 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125148
overall: 68451123200 mem 1714.647 user 203.995 sys 78.029 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.L006\tPU:L006\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: 78.064 sec; CPU: 1918.645 sec
sorting block 0, #reads = 125303 mem = 60297184 peak = 165277696
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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 7517831
output reads: 125303
bam_mem_sort: 1 calls 0.033 user 0.000 sys 0.041 real
bam_write: 1 calls 0.033 user 0.010 sys 0.035 real
execute: 1 calls 0.083 user 0.145 sys 78.499 real
merge_files: 1 calls 0.067 user 0.123 sys 0.325 real
parse_chunk: 2 calls 0.054 user 0.028 sys 0.091 real
read_chunk: 8 calls 0.022 user 0.045 sys 6.234 real
sort_block: 1 calls 0.121 user 0.056 sys 6.217 real
write_chunk: 4 calls 0.016 user 0.011 sys 0.042 real
overall: 476897280 mem 1.523 user 0.383 sys 78.520 real
ls: cannot access '*.cram': No such file or directory