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/ae/393d99a2c21d5b04e0f594cfce841e/.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/01/f6b177696fd9bc37f13734121f50ff/NTC_0002_0013_B23KGCJLT4_1/NTC_0002_0013_B23KGCJLT4_1_R1.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/ae/393d99a2c21d5b04e0f594cfce841e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/f6b177696fd9bc37f13734121f50ff/NTC_0002_0013_B23KGCJLT4_1/NTC_0002_0013_B23KGCJLT4_1_R2.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 NTC_0002_0013_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.
No more license available for sentieon:klib
version: sentieon-genomics-202308.03
No more license available for sentieon:klib
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
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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 1706.547 CPU sec, 1316.868 real sec
[M::process] read 472 sequences (71006 bp) in 0.000 CPU sec, 0.001 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 32, 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: (197, 302, 390)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 776)
[M::mem_pestat] mean and std.dev: (312.19, 151.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 969)
[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 472 reads in 0.565 CPU sec, 0.023 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: 472
overall: 68515672064 mem 1550.169 user 161.908 sys 1321.859 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_0013_B23KGCJLT4_1.L003\tPU:L003\tSM:NTC_0002_0013_B23KGCJLT4_1\tLB:NTC_0002_0013_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_0013_B23KGCJLT4_1_R1.fastq.gz NTC_0002_0013_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 1321.897 sec; CPU: 1712.081 sec
sorting block 0, #reads = 527 mem = 289118 peak = 77168640
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: 80858
output reads: 527
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.002 user 0.000 sys 0.002 real
execute: 1 calls 0.033 user 0.106 sys 1321.985 real
merge_files: 1 calls 0.023 user 0.078 sys 0.110 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
read_chunk: 4 calls 0.000 user 0.000 sys 4.969 real
sort_block: 1 calls 0.003 user 0.000 sys 4.969 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 264601600 mem 0.056 user 0.135 sys 1322.009 real
ls: cannot access '*.cram': No such file or directory