cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_BL.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 1485.399 CPU sec, 58.025 real sec
[M::process] read 125182 sequences (18067457 bp) in 0.205 CPU sec, 0.214 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44339, 0, 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: (186, 284, 405)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 843)
[M::mem_pestat] mean and std.dev: (307.42, 153.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1062)
[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 125182 reads in 11.501 CPU sec, 0.384 real sec
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125182
overall: 68458999808 mem 1377.846 user 125.055 sys 64.428 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:REGRESSION.HCC1395_BL.L004\tPU:L004\tSM:HCC1395_BL\tLB:HCC1395_BL\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 HCC1395_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 64.464 sec; CPU: 1502.903 sec
sorting block 0, #reads = 125334 mem = 59594110 peak = 166821888
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  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: 7367948
output reads: 125334
bam_mem_sort: 1 calls 0.019 user 0.000 sys 0.028 real
bam_write: 1 calls 0.020 user 0.010 sys 0.021 real
execute: 1 calls 0.081 user 0.156 sys 64.857 real
merge_files: 1 calls 0.069 user 0.120 sys 0.324 real
parse_chunk: 2 calls 0.063 user 0.027 sys 0.092 real
read_chunk: 7 calls 0.032 user 0.046 sys 5.947 real
sort_block: 1 calls 0.095 user 0.057 sys 5.887 real
write_chunk: 3 calls 0.021 user 0.012 sys 0.041 real
overall: 470708224 mem 1.479 user 0.448 sys 64.877 real
ls: cannot access '*.cram': No such file or directory