cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o NTC_0002_0015_A23MHWWLT4_1.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 1832.838 CPU sec, 72.940 real sec
[M::process] read 5064 sequences (761140 bp) in 0.001 CPU sec, 0.007 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 84, 0, 0)
[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: (139, 245, 321)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685)
[M::mem_pestat] mean and std.dev: (230.11, 110.36)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 867)
[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 5064 reads in 10.771 CPU sec, 0.354 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: 5064
overall: 68421234688 mem 1689.104 user 161.308 sys 80.103 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:A23MHWWLT4.NTC_0002_0015_A23MHWWLT4_1.L006\tPU:L006\tSM:NTC_0002_0015_A23MHWWLT4_1\tLB:NTC_0002_0015_A23MHWWLT4_1\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 NTC_0002_0015_A23MHWWLT4_1_R1.fastq.gz NTC_0002_0015_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 80.143 sec; CPU: 1850.414 sec
sorting block 0, #reads = 5218 mem = 2883572 peak = 81887232
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: 382148
output reads: 5218
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.001 real
bam_write: 1 calls 0.005 user 0.000 sys 0.004 real
execute: 1 calls 0.065 user 0.142 sys 80.303 real
merge_files: 1 calls 0.054 user 0.103 sys 0.172 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.004 real
read_chunk: 4 calls 0.003 user 0.001 sys 6.805 real
sort_block: 1 calls 0.012 user 0.000 sys 6.812 real
write_chunk: 1 calls 0.001 user 0.001 sys 0.002 real
overall: 270639104 mem 0.183 user 0.183 sys 80.325 real
ls: cannot access '*.cram': No such file or directory