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 1709.479 CPU sec, 61.870 real sec
[M::process] read 125182 sequences (18067457 bp) in 0.178 CPU sec, 0.184 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 24.190 CPU sec, 0.804 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125182
overall: 68444758016 mem 1561.138 user 178.758 sys 68.904 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: 68.952 sec; CPU: 1739.900 sec
sorting block 0, #reads = 125334 mem = 59594110 peak = 157360128
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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: util-sort
license: sentieon:util=1
output file size: 7367948
output reads: 125334
bam_mem_sort: 1 calls 0.019 user 0.001 sys 0.027 real
bam_write: 1 calls 0.058 user 0.011 sys 0.063 real
execute: 1 calls 0.064 user 0.131 sys 69.260 real
merge_files: 1 calls 0.050 user 0.101 sys 0.270 real
parse_chunk: 2 calls 0.043 user 0.012 sys 0.071 real
read_chunk: 7 calls 0.019 user 0.062 sys 6.168 real
sort_block: 1 calls 0.103 user 0.066 sys 6.163 real
write_chunk: 3 calls 0.010 user 0.021 sys 0.035 real
overall: 456974336 mem 1.271 user 0.382 sys 69.343 real
ls: cannot access '*.cram': No such file or directory