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/a7/f4269e34536e350f503f80abb7d9b3/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/a564cfdfe1f0b7a572356807999c15/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/a564cfdfe1f0b7a572356807999c15/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/f4269e34536e350f503f80abb7d9b3/HCC1395_BL/HCC1395_BL_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_BL.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 2646.148 CPU sec, 104.448 real sec
[M::process] read 125588 sequences (18133711 bp) in 0.171 CPU sec, 0.179 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44648, 0, 1)
[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: (188, 284, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (308.41, 153.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1064)
[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 125588 reads in 13.950 CPU sec, 0.463 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: 125588
overall: 67966636032 mem 2370.284 user 300.004 sys 115.111 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_BL.L005\tPU:L005\tSM:HCC1395_BL\tLB:HCC1395_BL\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_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 115.150 sec; CPU: 2670.291 sec
sorting block 0, #reads = 125732 mem = 59740910 peak = 160493568
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 384
algo: util-sort
license: sentieon:util=1
output file size: 7392989
output reads: 125732
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.028 real
bam_write: 1 calls 0.051 user 0.000 sys 0.051 real
execute: 1 calls 0.051 user 0.153 sys 115.521 real
merge_files: 1 calls 0.039 user 0.120 sys 0.273 real
parse_chunk: 2 calls 0.049 user 0.029 sys 0.086 real
read_chunk: 7 calls 0.027 user 0.053 sys 10.147 real
sort_block: 1 calls 0.123 user 0.051 sys 10.140 real
write_chunk: 3 calls 0.008 user 0.027 sys 0.041 real
overall: 457961472 mem 1.304 user 0.351 sys 115.542 real
ls: cannot access '*.cram': No such file or directory