This software is licensed to bgold@natera.com by Sentieon Inc.
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o NTC_0002_0009_B23KGCJLT4_1.bam --sam2bam -
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:klib
No more license available for sentieon:klib
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
[M::main_mem] bwa index loaded in 1552.535 CPU sec, 477.664 real sec
[M::process] read 1010 sequences (152386 bp) in 0.000 CPU sec, 0.002 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 3, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[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 1010 reads in 2.102 CPU sec, 0.073 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 1010
overall: 68528795648 mem 1385.748 user 175.139 sys 483.991 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:B23KGCJLT4.NTC_0002_0009_B23KGCJLT4_1.L002\tPU:L002\tSM:NTC_0002_0009_B23KGCJLT4_1\tLB:NTC_0002_0009_B23KGCJLT4_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_0009_B23KGCJLT4_1_R1.fastq.gz NTC_0002_0009_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 484.022 sec; CPU: 1560.889 sec
sorting block 0, #reads = 1059 mem = 589629 peak = 79888384
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: util-sort
license: sentieon:util=1
output file size: 110341
output reads: 1059
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.003 user 0.000 sys 0.003 real
execute: 1 calls 0.043 user 0.107 sys 484.120 real
merge_files: 1 calls 0.027 user 0.083 sys 0.121 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.001 real
read_chunk: 4 calls 0.004 user 0.000 sys 6.253 real
sort_block: 1 calls 0.005 user 0.000 sys 6.254 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 268591104 mem 0.115 user 0.098 sys 484.143 real
ls: cannot access '*.cram': No such file or directory