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/3f/f48c6b799ded91793d9481d3dd8609/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/74febdd24b414bbae81ec89d011d71/.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/7d/74febdd24b414bbae81ec89d011d71/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/f48c6b799ded91793d9481d3dd8609/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 2701.235 CPU sec, 92.763 real sec
[M::process] read 124904 sequences (18031367 bp) in 0.179 CPU sec, 0.183 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 44581, 0, 3)
[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, 282, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 840)
[M::mem_pestat] mean and std.dev: (307.00, 153.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1058)
[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 124904 reads in 15.452 CPU sec, 0.522 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: 124904
overall: 68016930816 mem 2514.901 user 212.174 sys 103.675 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.L007\tPU:L007\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: 103.710 sec; CPU: 2727.079 sec
sorting block 0, #reads = 125063 mem = 59373495 peak = 163667968
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 384
algo: util-sort
license: sentieon:util=1
output file size: 7316072
output reads: 125063
bam_mem_sort: 1 calls 0.037 user 0.000 sys 0.039 real
bam_write: 1 calls 0.042 user 0.000 sys 0.040 real
execute: 1 calls 0.064 user 0.150 sys 104.107 real
merge_files: 1 calls 0.048 user 0.123 sys 0.297 real
parse_chunk: 2 calls 0.099 user 0.003 sys 0.110 real
read_chunk: 7 calls 0.025 user 0.053 sys 10.340 real
sort_block: 1 calls 0.126 user 0.047 sys 10.322 real
write_chunk: 3 calls 0.023 user 0.008 sys 0.042 real
overall: 459956224 mem 1.586 user 0.331 sys 104.128 real
ls: cannot access '*.cram': No such file or directory