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 1840.136 CPU sec, 69.949 real sec
[M::process] read 27894 sequences (3951349 bp) in 0.060 CPU sec, 0.062 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 10696, 1, 1)
[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: (156, 229, 331)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)
[M::mem_pestat] mean and std.dev: (252.47, 124.59)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 856)
[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 27894 reads in 9.080 CPU sec, 0.305 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: 27894
overall: 68425953280 mem 1728.593 user 128.405 sys 78.052 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.L003\tPU:L003\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: 78.092 sec; CPU: 1857.001 sec
sorting block 0, #reads = 28102 mem = 13967316 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: 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: 2186017
output reads: 28102
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.006 real
bam_write: 1 calls 0.012 user 0.013 sys 0.019 real
execute: 1 calls 0.047 user 0.136 sys 78.298 real
merge_files: 1 calls 0.025 user 0.113 sys 0.181 real
parse_chunk: 1 calls 0.009 user 0.010 sys 0.023 real
read_chunk: 4 calls 0.000 user 0.022 sys 7.756 real
sort_block: 1 calls 0.022 user 0.044 sys 7.778 real
write_chunk: 1 calls 0.000 user 0.001 sys 0.008 real
overall: 305995776 mem 0.425 user 0.244 sys 78.320 real
ls: cannot access '*.cram': No such file or directory