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/2a/9a35d14473f366ddc5b52923914ca6/.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/84/56616c1a84f47a3347acb8b5b8fea6/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/2a/9a35d14473f366ddc5b52923914ca6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/56616c1a84f47a3347acb8b5b8fea6/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 1938.224 CPU sec, 71.528 real sec
[M::process] read 124560 sequences (17940725 bp) in 0.168 CPU sec, 0.172 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 11.032 CPU sec, 0.371 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124560
overall: 68438474752 mem 1715.825 user 242.915 sys 81.383 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: 81.473 sec; CPU: 1958.742 sec
sorting block 0, #reads = 124723 mem = 59715543 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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 7289742
output reads: 124723
bam_mem_sort: 1 calls 0.024 user 0.000 sys 0.033 real
bam_write: 1 calls 0.111 user 0.018 sys 0.128 real
execute: 1 calls 0.063 user 0.145 sys 81.889 real
merge_files: 1 calls 0.036 user 0.128 sys 0.291 real
parse_chunk: 2 calls 0.051 user 0.015 sys 0.076 real
read_chunk: 8 calls 0.031 user 0.029 sys 9.437 real
sort_block: 1 calls 0.187 user 0.059 sys 9.506 real
write_chunk: 4 calls 0.013 user 0.030 sys 0.074 real
overall: 461094912 mem 1.278 user 0.357 sys 81.965 real
ls: cannot access '*.cram': No such file or directory