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/e9/0da060fbb1533941a0ba888257229e/.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-rnd-pltf-dev-nextflow-scratch-01/work/c4/fb0cd825eae9f9a0aa12fda9230086/HCC1395_tumor/HCC1395_tumor_R2.fastq.gz
  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/e9/0da060fbb1533941a0ba888257229e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/fb0cd825eae9f9a0aa12fda9230086/HCC1395_tumor/HCC1395_tumor_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_tumor.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 1638.085 CPU sec, 57.985 real sec
[M::process] read 124560 sequences (17940725 bp) in 0.174 CPU sec, 0.180 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 43403, 0, 7)
[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: (181, 272, 392)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 814)
[M::mem_pestat] mean and std.dev: (297.87, 148.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1025)
[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 124560 reads in 16.393 CPU sec, 0.557 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: 124560
overall: 68466823168 mem 1517.183 user 142.948 sys 64.203 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_tumor.L004\tPU:L004\tSM:HCC1395_tumor\tLB:HCC1395_tumor\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_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 64.238 sec; CPU: 1660.134 sec
sorting block 0, #reads = 124723 mem = 59715543 peak = 166821888
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 192
algo: util-sort
license: sentieon:util=1
output file size: 7289742
output reads: 124723
bam_mem_sort: 1 calls 0.029 user 0.001 sys 0.030 real
bam_write: 1 calls 0.022 user 0.001 sys 0.023 real
execute: 1 calls 0.061 user 0.130 sys 64.573 real
merge_files: 1 calls 0.044 user 0.105 sys 0.270 real
parse_chunk: 2 calls 0.068 user 0.006 sys 0.082 real
read_chunk: 8 calls 0.026 user 0.032 sys 5.612 real
sort_block: 1 calls 0.098 user 0.029 sys 5.565 real
write_chunk: 4 calls 0.008 user 0.015 sys 0.036 real
overall: 469565440 mem 1.342 user 0.381 sys 64.594 real
ls: cannot access '*.cram': No such file or directory