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/e5/0f1ade856feb0e4da65c3b5fd52271/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/c5c52435c3972da9f3cf0df8a9106c/HCC1395_tumor/HCC1395_tumor_R2.fastq.gz
  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/e5/0f1ade856feb0e4da65c3b5fd52271/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/c5c52435c3972da9f3cf0df8a9106c/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 2348.462 CPU sec, 97.845 real sec
[M::process] read 125626 sequences (18098646 bp) in 0.176 CPU sec, 0.177 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 44052, 2, 4)
[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: (182, 274, 395)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 821)
[M::mem_pestat] mean and std.dev: (299.15, 150.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1034)
[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 125626 reads in 43.560 CPU sec, 1.436 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: 125626
overall: 68306345984 mem 1970.122 user 431.597 sys 108.974 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.L002\tPU:L002\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: 109.036 sec; CPU: 2401.721 sec
sorting block 0, #reads = 125801 mem = 60183308 peak = 160432128
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: 7344186
output reads: 125801
bam_mem_sort: 1 calls 0.027 user 0.002 sys 0.034 real
bam_write: 1 calls 0.099 user 0.005 sys 0.101 real
execute: 1 calls 0.068 user 0.131 sys 109.427 real
merge_files: 1 calls 0.049 user 0.102 sys 0.271 real
parse_chunk: 2 calls 0.036 user 0.038 sys 0.080 real
read_chunk: 8 calls 0.040 user 0.057 sys 9.637 real
sort_block: 1 calls 0.160 user 0.072 sys 9.688 real
write_chunk: 4 calls 0.022 user 0.007 sys 0.040 real
overall: 469618688 mem 1.179 user 0.431 sys 109.486 real
ls: cannot access '*.cram': No such file or directory