cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_BL.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 2485.804 CPU sec, 96.460 real sec
[M::process] read 124700 sequences (17992902 bp) in 0.172 CPU sec, 0.175 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 44507, 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: (186, 282, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 849)
[M::mem_pestat] mean and std.dev: (307.31, 153.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1070)
[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 124700 reads in 40.678 CPU sec, 1.337 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: 124700
overall: 68353540096 mem 2031.273 user 504.781 sys 107.362 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_BL.L002\tPU:L002\tSM:HCC1395_BL\tLB:HCC1395_BL\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_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 107.418 sec; CPU: 2536.057 sec
sorting block 0, #reads = 124816 mem = 59282090 peak = 163676160
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 384
algo: util-sort
license: sentieon:util=1
output file size: 7313733
output reads: 124816
bam_mem_sort: 1 calls 0.027 user 0.000 sys 0.032 real
bam_write: 1 calls 0.090 user 0.000 sys 0.089 real
execute: 1 calls 0.049 user 0.138 sys 107.781 real
merge_files: 1 calls 0.038 user 0.107 sys 0.261 real
parse_chunk: 2 calls 0.038 user 0.035 sys 0.077 real
read_chunk: 7 calls 0.040 user 0.044 sys 9.503 real
sort_block: 1 calls 0.153 user 0.061 sys 9.542 real
write_chunk: 3 calls 0.000 user 0.024 sys 0.035 real
overall: 457719808 mem 1.259 user 0.347 sys 107.839 real
ls: cannot access '*.cram': No such file or directory