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/33/cc867d7984eec298d1d104007a2cb4/.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/36/90e478b00827b3e49493314b20929b/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/33/cc867d7984eec298d1d104007a2cb4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/90e478b00827b3e49493314b20929b/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 1966.274 CPU sec, 76.357 real sec
[M::process] read 124464 sequences (17920568 bp) in 0.205 CPU sec, 0.213 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 43611, 0, 5)
[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, 272, 391)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 813)
[M::mem_pestat] mean and std.dev: (297.21, 149.05)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1024)
[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 124464 reads in 11.314 CPU sec, 0.378 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124464
overall: 68430643200 mem 1843.688 user 142.066 sys 84.939 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.L003\tPU:L003\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: 84.982 sec; CPU: 1985.756 sec
sorting block 0, #reads = 124643 mem = 59577413 peak = 165306368
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 7263380
output reads: 124643
bam_mem_sort: 1 calls 0.027 user 0.000 sys 0.028 real
bam_write: 1 calls 0.020 user 0.000 sys 0.020 real
execute: 1 calls 0.041 user 0.175 sys 85.349 real
merge_files: 1 calls 0.016 user 0.152 sys 0.303 real
parse_chunk: 2 calls 0.082 user 0.000 sys 0.089 real
read_chunk: 7 calls 0.023 user 0.064 sys 8.128 real
sort_block: 1 calls 0.085 user 0.066 sys 8.076 real
write_chunk: 3 calls 0.000 user 0.027 sys 0.031 real
overall: 470437888 mem 1.538 user 0.266 sys 85.373 real
ls: cannot access '*.cram': No such file or directory