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 1618.722 CPU sec, 56.272 real sec
[M::process] read 124736 sequences (18072176 bp) in 0.165 CPU sec, 0.173 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44863, 0, 1)
[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: (189, 289, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (315.26, 157.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1101)
[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 124736 reads in 10.269 CPU sec, 0.343 real sec
os version: Linux 6.12.83
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: 124736
overall: 68525056000 mem 1510.449 user 124.281 sys 62.355 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.L007\tPU:L007\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: 62.389 sec; CPU: 1634.733 sec
sorting block 0, #reads = 124877 mem = 60037142 peak = 166858752
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 7455819
output reads: 124877
bam_mem_sort: 1 calls 0.026 user 0.000 sys 0.030 real
bam_write: 1 calls 0.082 user 0.000 sys 0.083 real
execute: 1 calls 0.037 user 0.133 sys 62.764 real
merge_files: 1 calls 0.022 user 0.111 sys 0.248 real
parse_chunk: 2 calls 0.054 user 0.009 sys 0.070 real
read_chunk: 8 calls 0.049 user 0.033 sys 5.683 real
sort_block: 1 calls 0.162 user 0.030 sys 5.713 real
write_chunk: 4 calls 0.000 user 0.020 sys 0.031 real
overall: 478863360 mem 1.202 user 0.330 sys 62.784 real
ls: cannot access '*.cram': No such file or directory