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/be/715d0e3eecc625b329d3b5f78979f8/.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/7a/e358b67bf6fe85f56c92a2b23f2a19/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/be/715d0e3eecc625b329d3b5f78979f8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/e358b67bf6fe85f56c92a2b23f2a19/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 1593.224 CPU sec, 57.070 real sec
[M::process] read 124926 sequences (17971193 bp) in 0.176 CPU sec, 0.178 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 43938, 1, 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: (181, 272, 393)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 817)
[M::mem_pestat] mean and std.dev: (297.73, 149.70)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1029)
[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 124926 reads in 20.923 CPU sec, 0.691 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: 124926
overall: 68485709824 mem 1484.327 user 135.527 sys 63.475 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.L005\tPU:L005\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: 63.555 sec; CPU: 1619.857 sec
sorting block 0, #reads = 125074 mem = 59766436 peak = 166875136
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: 7280382
output reads: 125074
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.028 real
bam_write: 1 calls 0.024 user 0.008 sys 0.029 real
execute: 1 calls 0.058 user 0.114 sys 63.825 real
merge_files: 1 calls 0.042 user 0.092 sys 0.253 real
parse_chunk: 2 calls 0.069 user 0.009 sys 0.094 real
read_chunk: 8 calls 0.020 user 0.044 sys 5.660 real
sort_block: 1 calls 0.088 user 0.039 sys 5.625 real
write_chunk: 4 calls 0.008 user 0.009 sys 0.027 real
overall: 483028992 mem 1.366 user 0.235 sys 63.896 real
ls: cannot access '*.cram': No such file or directory