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/4c/ef8cdc2b4c9c7d4144c5c9fe48f288/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/774c7f21902859e1cde06f01fb5bfa/NTC_0002_0010_B23KGCJLT4_1/NTC_0002_0010_B23KGCJLT4_1_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/ae/774c7f21902859e1cde06f01fb5bfa/NTC_0002_0010_B23KGCJLT4_1/NTC_0002_0010_B23KGCJLT4_1_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/ef8cdc2b4c9c7d4144c5c9fe48f288/.command.run
==> STAGING COMPLETE (7 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o NTC_0002_0010_B23KGCJLT4_1.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
No more license available for sentieon:klib
No more license available for sentieon:klib
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
No more license available for sentieon:klib
[M::main_mem] bwa index loaded in 1889.356 CPU sec, 1453.970 real sec
[M::process] read 816 sequences (122880 bp) in 0.000 CPU sec, 0.001 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 2, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[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 816 reads in 1.496 CPU sec, 0.057 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: 816
overall: 68487352320 mem 1625.158 user 271.139 sys 1459.478 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:B23KGCJLT4.NTC_0002_0010_B23KGCJLT4_1.L003\tPU:L003\tSM:NTC_0002_0010_B23KGCJLT4_1\tLB:NTC_0002_0010_B23KGCJLT4_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 NTC_0002_0010_B23KGCJLT4_1_R1.fastq.gz NTC_0002_0010_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 1459.517 sec; CPU: 1896.300 sec
sorting block 0, #reads = 846 mem = 470765 peak = 77160448
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: 93998
output reads: 846
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.003 user 0.000 sys 0.003 real
execute: 1 calls 0.044 user 0.118 sys 1459.632 real
merge_files: 1 calls 0.033 user 0.089 sys 0.133 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.001 real
read_chunk: 4 calls 0.001 user 0.000 sys 5.453 real
sort_block: 1 calls 0.004 user 0.000 sys 5.454 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 264540160 mem 0.067 user 0.153 sys 1459.654 real
ls: cannot access '*.cram': No such file or directory