cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_eKx-T1-TDNA-1_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 1804.472 CPU sec, 63.191 real sec
[M::process] read 28426 sequences (4020997 bp) in 0.045 CPU sec, 0.053 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 10833, 0, 6)
[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: (153, 225, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 687)
[M::mem_pestat] mean and std.dev: (251.22, 126.06)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 865)
[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 28426 reads in 10.850 CPU sec, 0.372 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: 28426
overall: 68435443712 mem 1610.914 user 210.279 sys 69.439 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_eKx-T1-TDNA-1_A23MHWWLT4_1.L001\tPU:L001\tSM:659_eKx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_eKx-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_eKx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_eKx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 69.476 sec; CPU: 1821.195 sec
sorting block 0, #reads = 28664 mem = 14264180 peak = 103907328
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 192
algo: util-sort
license: sentieon:util=1
output file size: 2216907
output reads: 28664
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.005 real
bam_write: 1 calls 0.013 user 0.009 sys 0.016 real
execute: 1 calls 0.046 user 0.103 sys 69.642 real
merge_files: 1 calls 0.037 user 0.073 sys 0.153 real
parse_chunk: 1 calls 0.013 user 0.000 sys 0.016 real
read_chunk: 4 calls 0.003 user 0.012 sys 5.845 real
sort_block: 1 calls 0.029 user 0.019 sys 5.857 real
write_chunk: 1 calls 0.007 user 0.000 sys 0.007 real
overall: 302829568 mem 0.438 user 0.164 sys 69.665 real
ls: cannot access '*.cram': No such file or directory