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 2461.498 CPU sec, 85.711 real sec
[M::process] read 125750 sequences (18108531 bp) in 0.172 CPU sec, 0.178 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 43991, 1, 3)
[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: (182, 273, 393)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 815)
[M::mem_pestat] mean and std.dev: (298.32, 149.58)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1026)
[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 125750 reads in 20.539 CPU sec, 0.681 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: 125750
overall: 68174278656 mem 2108.642 user 378.832 sys 91.837 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.L008\tPU:L008\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: 91.872 sec; CPU: 2487.476 sec
sorting block 0, #reads = 125912 mem = 60232803 peak = 160456704
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 384
algo: util-sort
license: sentieon:util=1
output file size: 7336702
output reads: 125912
bam_mem_sort: 1 calls 0.024 user 0.000 sys 0.030 real
bam_write: 1 calls 0.050 user 0.009 sys 0.058 real
execute: 1 calls 0.062 user 0.144 sys 92.279 real
merge_files: 1 calls 0.048 user 0.115 sys 0.295 real
parse_chunk: 2 calls 0.067 user 0.009 sys 0.084 real
read_chunk: 8 calls 0.048 user 0.038 sys 5.394 real
sort_block: 1 calls 0.138 user 0.037 sys 5.393 real
write_chunk: 4 calls 0.006 user 0.025 sys 0.054 real
overall: 451928064 mem 1.347 user 0.355 sys 92.296 real
ls: cannot access '*.cram': No such file or directory