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 1883.807 CPU sec, 65.685 real sec
[M::process] read 29568 sequences (4179011 bp) in 0.035 CPU sec, 0.039 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 11273, 1, 7)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (251, 318, 318)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (117, 452)
[M::mem_pestat] mean and std.dev: (277.17, 43.39)
[M::mem_pestat] low and high boundaries for proper pairs: (50, 519)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (153, 225, 323)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 663)
[M::mem_pestat] mean and std.dev: (247.98, 122.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 833)
[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_pestat] skip orientation FF
[M::mem_process_seqs] Processed 29568 reads in 10.038 CPU sec, 0.344 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: 29568
overall: 68438593536 mem 1736.656 user 163.368 sys 72.211 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.L002\tPU:L002\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: 72.251 sec; CPU: 1900.027 sec
sorting block 0, #reads = 29820 mem = 14871408 peak = 107053056
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: 2320054
output reads: 29820
bam_mem_sort: 1 calls 0.006 user 0.000 sys 0.010 real
bam_write: 1 calls 0.015 user 0.002 sys 0.013 real
execute: 1 calls 0.061 user 0.150 sys 72.508 real
merge_files: 1 calls 0.044 user 0.124 sys 0.222 real
parse_chunk: 1 calls 0.022 user 0.008 sys 0.034 real
read_chunk: 4 calls 0.009 user 0.006 sys 6.178 real
sort_block: 1 calls 0.052 user 0.017 sys 6.200 real
write_chunk: 1 calls 0.000 user 0.007 sys 0.010 real
overall: 308039680 mem 0.579 user 0.224 sys 72.529 real
ls: cannot access '*.cram': No such file or directory