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 1769.422 CPU sec, 61.119 real sec
[M::process] read 125052 sequences (17995734 bp) in 0.192 CPU sec, 0.198 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 43482, 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, 272, 393)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 819)
[M::mem_pestat] mean and std.dev: (297.47, 149.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1032)
[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 125052 reads in 16.229 CPU sec, 0.558 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: 125052
overall: 68495196160 mem 1661.035 user 130.610 sys 67.689 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.L006\tPU:L006\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: 67.758 sec; CPU: 1791.647 sec
sorting block 0, #reads = 125216 mem = 59825649 peak = 165216256
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: 7277935
output reads: 125216
bam_mem_sort: 1 calls 0.027 user 0.002 sys 0.032 real
bam_write: 1 calls 0.068 user 0.022 sys 0.091 real
execute: 1 calls 0.057 user 0.150 sys 68.159 real
merge_files: 1 calls 0.030 user 0.123 sys 0.285 real
parse_chunk: 2 calls 0.092 user 0.017 sys 0.119 real
read_chunk: 8 calls 0.027 user 0.052 sys 5.938 real
sort_block: 1 calls 0.121 user 0.093 sys 5.964 real
write_chunk: 4 calls 0.000 user 0.033 sys 0.049 real
overall: 477741056 mem 1.371 user 0.349 sys 68.204 real
ls: cannot access '*.cram': No such file or directory