Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/4f39334c1ddba90590d42dad60a6bc/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/e1c17bf1ef42130ec4a8b769e83e10/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/e1c17bf1ef42130ec4a8b769e83e10/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/4f39334c1ddba90590d42dad60a6bc/HCC1395_BL/HCC1395_BL_R1.fastq.gz
==> STAGING COMPLETE (7 inputs)

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 2067.532 CPU sec, 81.924 real sec
[M::process] read 125182 sequences (18067457 bp) in 0.168 CPU sec, 0.175 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 12.451 CPU sec, 0.412 real sec
os version: Linux 6.12.83
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: 68424392704 mem 1874.628 user 211.866 sys 88.858 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: 88.912 sec; CPU: 2086.497 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: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 7367948
output reads: 125334
bam_mem_sort: 1 calls 0.022 user 0.000 sys 0.026 real
bam_write: 1 calls 0.049 user 0.010 sys 0.056 real
execute: 1 calls 0.066 user 0.106 sys 89.233 real
merge_files: 1 calls 0.047 user 0.087 sys 0.252 real
parse_chunk: 2 calls 0.045 user 0.017 sys 0.074 real
read_chunk: 7 calls 0.046 user 0.050 sys 6.468 real
sort_block: 1 calls 0.101 user 0.060 sys 6.466 real
write_chunk: 3 calls 0.013 user 0.007 sys 0.028 real
overall: 475787264 mem 1.299 user 0.277 sys 89.280 real
ls: cannot access '*.cram': No such file or directory