cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_tumor.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 1661.592 CPU sec, 58.673 real sec
[M::process] read 124478 sequences (17924843 bp) in 0.170 CPU sec, 0.173 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 43537, 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: (180, 274, 394)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 822)
[M::mem_pestat] mean and std.dev: (298.63, 150.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1036)
[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 124478 reads in 12.725 CPU sec, 0.428 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: 124478
overall: 68504539136 mem 1528.899 user 151.385 sys 65.070 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.HCC1395_tumor.L001\tPU:L001\tSM:HCC1395_tumor\tLB:HCC1395_tumor\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 HCC1395_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 65.108 sec; CPU: 1680.287 sec
sorting block 0, #reads = 124658 mem = 59579630 peak = 168386560
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: 7258879
output reads: 124658
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.028 real
bam_write: 1 calls 0.064 user 0.008 sys 0.073 real
execute: 1 calls 0.052 user 0.128 sys 65.474 real
merge_files: 1 calls 0.037 user 0.095 sys 0.248 real
parse_chunk: 2 calls 0.039 user 0.017 sys 0.071 real
read_chunk: 7 calls 0.034 user 0.056 sys 5.915 real
sort_block: 1 calls 0.128 user 0.056 sys 5.931 real
write_chunk: 3 calls 0.015 user 0.009 sys 0.034 real
overall: 471904256 mem 1.216 user 0.288 sys 65.497 real
ls: cannot access '*.cram': No such file or directory