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 1420.203 CPU sec, 49.005 real sec
[M::process] read 124736 sequences (18072176 bp) in 0.162 CPU sec, 0.170 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 9.893 CPU sec, 0.330 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: 124736
overall: 68528234496 mem 1346.144 user 89.040 sys 54.430 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: 54.468 sec; CPU: 1435.187 sec
sorting block 0, #reads = 124877 mem = 60037142 peak = 168439808
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 192
algo: util-sort
license: sentieon:util=1
output file size: 7455819
output reads: 124877
bam_mem_sort: 1 calls 0.020 user 0.000 sys 0.026 real
bam_write: 1 calls 0.109 user 0.000 sys 0.111 real
execute: 1 calls 0.067 user 0.092 sys 54.857 real
merge_files: 1 calls 0.043 user 0.080 sys 0.244 real
parse_chunk: 2 calls 0.076 user 0.001 sys 0.095 real
read_chunk: 8 calls 0.047 user 0.037 sys 5.044 real
sort_block: 1 calls 0.173 user 0.038 sys 5.094 real
write_chunk: 4 calls 0.001 user 0.012 sys 0.028 real
overall: 488345600 mem 1.371 user 0.201 sys 54.881 real
ls: cannot access '*.cram': No such file or directory