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/bd/75de5543d3a1656e8c195853268882/.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/55/3c121f3fe7450f29ccaac3b5e02b78/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/bd/75de5543d3a1656e8c195853268882/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/3c121f3fe7450f29ccaac3b5e02b78/HCC1395_tumor/HCC1395_tumor_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_tumor.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 1627.597 CPU sec, 58.250 real sec
[M::process] read 124478 sequences (17924843 bp) in 0.163 CPU sec, 0.172 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 43537, 0, 2)
[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: (180, 274, 394)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 822)
[M::mem_pestat] mean and std.dev: (298.63, 150.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1036)
[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 124478 reads in 22.653 CPU sec, 0.753 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: 124478
overall: 68476313600 mem 1491.187 user 164.862 sys 64.804 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.L001\tPU:L001\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: 64.845 sec; CPU: 1656.051 sec
sorting block 0, #reads = 124658 mem = 59579630 peak = 168394752
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: 7258879
output reads: 124658
bam_mem_sort: 1 calls 0.028 user 0.000 sys 0.029 real
bam_write: 1 calls 0.069 user 0.000 sys 0.071 real
execute: 1 calls 0.073 user 0.100 sys 65.206 real
merge_files: 1 calls 0.045 user 0.089 sys 0.247 real
parse_chunk: 2 calls 0.040 user 0.023 sys 0.069 real
read_chunk: 7 calls 0.043 user 0.029 sys 5.750 real
sort_block: 1 calls 0.140 user 0.032 sys 5.762 real
write_chunk: 3 calls 0.009 user 0.012 sys 0.029 real
overall: 470577152 mem 1.233 user 0.262 sys 65.224 real
ls: cannot access '*.cram': No such file or directory