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 1618.815 CPU sec, 57.197 real sec
[M::process] read 125346 sequences (18175258 bp) in 0.185 CPU sec, 0.192 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 45082, 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: (192, 292, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (316.67, 156.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1100)
[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 125346 reads in 12.385 CPU sec, 0.433 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: 125346
overall: 68499865600 mem 1511.350 user 126.956 sys 64.754 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.L004\tPU:L004\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: 64.791 sec; CPU: 1638.309 sec
sorting block 0, #reads = 125458 mem = 60226619 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: 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: 7445623
output reads: 125458
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.028 real
bam_write: 1 calls 0.119 user 0.000 sys 0.124 real
execute: 1 calls 0.082 user 0.111 sys 65.238 real
merge_files: 1 calls 0.070 user 0.081 sys 0.277 real
parse_chunk: 2 calls 0.046 user 0.034 sys 0.087 real
read_chunk: 8 calls 0.042 user 0.041 sys 7.056 real
sort_block: 1 calls 0.184 user 0.058 sys 7.122 real
write_chunk: 4 calls 0.013 user 0.010 sys 0.040 real
overall: 479514624 mem 1.353 user 0.322 sys 65.261 real
ls: cannot access '*.cram': No such file or directory