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.
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 1790.076 CPU sec, 63.546 real sec
[M::process] read 65780 sequences (9044241 bp) in 0.102 CPU sec, 0.108 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 25158, 8, 17)
[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: (130, 180, 255)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 505)
[M::mem_pestat] mean and std.dev: (199.05, 92.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 630)
[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: (129, 289, 627)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1623)
[M::mem_pestat] mean and std.dev: (367.59, 287.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 2121)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 65780 reads in 21.457 CPU sec, 0.718 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: 65780
overall: 68460539904 mem 1676.330 user 141.881 sys 70.954 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.L003\tPU:L003\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: 70.993 sec; CPU: 1818.214 sec
sorting block 0, #reads = 66479 mem = 32897487 peak = 138510336
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: 5059462
output reads: 66479
bam_mem_sort: 1 calls 0.011 user 0.000 sys 0.017 real
bam_write: 1 calls 0.038 user 0.009 sys 0.041 real
execute: 1 calls 0.050 user 0.143 sys 71.325 real
merge_files: 1 calls 0.030 user 0.119 sys 0.246 real
parse_chunk: 1 calls 0.045 user 0.000 sys 0.054 real
read_chunk: 5 calls 0.005 user 0.035 sys 6.671 real
sort_block: 1 calls 0.101 user 0.040 sys 6.691 real
write_chunk: 2 calls 0.000 user 0.017 sys 0.020 real
overall: 369254400 mem 0.953 user 0.331 sys 71.350 real
ls: cannot access '*.cram': No such file or directory