Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/b74c4f54a0283c9b1e89b643511b8c/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  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/78/d3f3ca2f9a6e3713d0981d788aedef/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/92/b74c4f54a0283c9b1e89b643511b8c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/d3f3ca2f9a6e3713d0981d788aedef/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 1442.024 CPU sec, 49.401 real sec
[M::process] read 125124 sequences (17999868 bp) in 0.198 CPU sec, 0.203 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 43763, 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: (180, 272, 391)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 813)
[M::mem_pestat] mean and std.dev: (296.95, 149.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1024)
[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 125124 reads in 10.761 CPU sec, 0.360 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125124
overall: 68551806976 mem 1399.623 user 58.921 sys 55.531 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.L007\tPU:L007\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: 55.567 sec; CPU: 1458.547 sec
sorting block 0, #reads = 125293 mem = 59924104 peak = 169246720
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 96
algo: util-sort
license: sentieon:util=1
output file size: 7303558
output reads: 125293
bam_mem_sort: 1 calls 0.022 user 0.002 sys 0.024 real
bam_write: 1 calls 0.114 user 0.000 sys 0.121 real
execute: 1 calls 0.061 user 0.111 sys 55.978 real
merge_files: 1 calls 0.049 user 0.083 sys 0.255 real
parse_chunk: 2 calls 0.049 user 0.015 sys 0.071 real
read_chunk: 8 calls 0.042 user 0.031 sys 5.685 real
sort_block: 1 calls 0.179 user 0.028 sys 5.742 real
write_chunk: 4 calls 0.005 user 0.010 sys 0.029 real
overall: 496951296 mem 1.356 user 0.204 sys 56.000 real
ls: cannot access '*.cram': No such file or directory