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 659_Lx-T1-TDNA-1_A23MHWWLT4_1.bam --sam2bam -
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 2665.772 CPU sec, 109.863 real sec
[M::process] read 63760 sequences (8756603 bp) in 0.079 CPU sec, 0.089 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 24349, 5, 20)
[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: (129, 180, 256)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 510)
[M::mem_pestat] mean and std.dev: (199.26, 92.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 637)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (253, 1017, 3256)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9262)
[M::mem_pestat] mean and std.dev: (1447.00, 1419.96)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 12265)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 63760 reads in 26.373 CPU sec, 0.874 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: 63760
overall: 68045258752 mem 2073.456 user 630.885 sys 122.934 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:A23MHWWLT4.659_Lx-T1-TDNA-1_A23MHWWLT4_1.L005\tPU:L005\tSM:659_Lx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_Lx-T1-TDNA-1_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.64 659_Lx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_Lx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 122.968 sec; CPU: 2704.344 sec
sorting block 0, #reads = 64400 mem = 32031737 peak = 132194304
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: 5057515
output reads: 64400
bam_mem_sort: 1 calls 0.019 user 0.000 sys 0.019 real
bam_write: 1 calls 0.015 user 0.001 sys 0.018 real
execute: 1 calls 0.060 user 0.131 sys 123.267 real
merge_files: 1 calls 0.020 user 0.122 sys 0.224 real
parse_chunk: 1 calls 0.042 user 0.015 sys 0.059 real
read_chunk: 5 calls 0.007 user 0.040 sys 12.184 real
sort_block: 1 calls 0.076 user 0.047 sys 12.198 real
write_chunk: 2 calls 0.000 user 0.015 sys 0.022 real
overall: 324288512 mem 0.861 user 0.328 sys 123.288 real
ls: cannot access '*.cram': No such file or directory