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/ec/77c1118bb3acc540288187d841e707/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/46723e98c180739846d76286b08b6f/.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/b3/46723e98c180739846d76286b08b6f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/77c1118bb3acc540288187d841e707/HCC1395_BL/HCC1395_BL_R1.fastq.gz
==> STAGING COMPLETE (7 inputs)

This software is licensed to bgold@natera.com by Sentieon Inc.
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.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 2616.933 CPU sec, 96.903 real sec
[M::process] read 125182 sequences (18067457 bp) in 0.171 CPU sec, 0.178 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 24.985 CPU sec, 0.817 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: 68117655552 mem 2180.896 user 467.832 sys 104.541 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: 104.567 sec; CPU: 2648.731 sec
sorting block 0, #reads = 125334 mem = 59594110 peak = 163651584
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 0.028 user 0.000 sys 0.033 real
bam_write: 1 calls 0.019 user 0.013 sys 0.028 real
execute: 1 calls 0.080 user 0.150 sys 104.955 real
merge_files: 1 calls 0.058 user 0.126 sys 0.305 real
parse_chunk: 2 calls 0.074 user 0.027 sys 0.103 real
read_chunk: 7 calls 0.052 user 0.031 sys 6.772 real
sort_block: 1 calls 0.102 user 0.041 sys 6.732 real
write_chunk: 3 calls 0.016 user 0.028 sys 0.051 real
overall: 444850176 mem 1.501 user 0.307 sys 104.970 real
ls: cannot access '*.cram': No such file or directory