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 1592.779 CPU sec, 56.996 real sec
[M::process] read 124610 sequences (17629509 bp) in 0.168 CPU sec, 0.170 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 46577, 0, 2)
[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, 319)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 649)
[M::mem_pestat] mean and std.dev: (246.13, 119.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 814)
[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 124610 reads in 18.183 CPU sec, 0.598 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: 124610
overall: 68504641536 mem 1475.902 user 141.949 sys 64.489 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.L005\tPU:L005\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: 64.526 sec; CPU: 1617.853 sec
sorting block 0, #reads = 124855 mem = 59334865 peak = 166838272
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: 7013233
output reads: 124855
bam_mem_sort: 1 calls 0.027 user 0.000 sys 0.028 real
bam_write: 1 calls 0.068 user 0.001 sys 0.072 real
execute: 1 calls 0.075 user 0.117 sys 64.905 real
merge_files: 1 calls 0.051 user 0.093 sys 0.264 real
parse_chunk: 2 calls 0.036 user 0.028 sys 0.071 real
read_chunk: 7 calls 0.033 user 0.034 sys 6.848 real
sort_block: 1 calls 0.113 user 0.057 sys 6.856 real
write_chunk: 3 calls 0.020 user 0.007 sys 0.033 real
overall: 471363584 mem 1.231 user 0.313 sys 64.925 real
ls: cannot access '*.cram': No such file or directory