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/7b/c72f68160a59a95cba31e64673ebdf/.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/cb/014d4f38492d55be65e4b56cc02321/659_eKx-T1-TDNA-1_A23MHWWLT4_1/659_eKx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/014d4f38492d55be65e4b56cc02321/659_eKx-T1-TDNA-1_A23MHWWLT4_1/659_eKx-T1-TDNA-1_A23MHWWLT4_1_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/7b/c72f68160a59a95cba31e64673ebdf/.command.run
==> STAGING COMPLETE (7 inputs)

This software is licensed to bgold@natera.com by Sentieon Inc.
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_eKx-T1-TDNA-1_A23MHWWLT4_1.bam --sam2bam -
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 2800.069 CPU sec, 114.444 real sec
[M::process] read 28076 sequences (3974119 bp) in 0.040 CPU sec, 0.042 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 10816, 0, 0)
[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: (152, 222, 321)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 659)
[M::mem_pestat] mean and std.dev: (246.21, 120.41)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 828)
[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 28076 reads in 21.231 CPU sec, 0.707 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: 28076
overall: 68035829760 mem 2199.597 user 633.422 sys 126.894 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:A23MHWWLT4.659_eKx-T1-TDNA-1_A23MHWWLT4_1.L005\tPU:L005\tSM:659_eKx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_eKx-T1-TDNA-1_A23MHWWLT4_1\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.64 659_eKx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_eKx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 126.925 sec; CPU: 2833.022 sec
sorting block 0, #reads = 28299 mem = 14021361 peak = 100663296
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: 2239777
output reads: 28299
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.006 real
bam_write: 1 calls 0.010 user 0.006 sys 0.010 real
execute: 1 calls 0.075 user 0.125 sys 127.142 real
merge_files: 1 calls 0.064 user 0.092 sys 0.200 real
parse_chunk: 1 calls 0.000 user 0.018 sys 0.019 real
read_chunk: 4 calls 0.005 user 0.014 sys 11.724 real
sort_block: 1 calls 0.010 user 0.039 sys 11.729 real
write_chunk: 1 calls 0.004 user 0.000 sys 0.009 real
overall: 301981696 mem 0.455 user 0.227 sys 127.160 real
ls: cannot access '*.cram': No such file or directory