cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_ezg-N1-BDNA-1_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
[M::main_mem] bwa index loaded in 1663.935 CPU sec, 715.889 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: 0
overall: 68504612864 mem 1515.842 user 154.327 sys 722.113 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:B23KGCJLT4.659_ezg-N1-BDNA-1_B23KGCJLT4_1.L003\tPU:L003\tSM:659_ezg-N1-BDNA-1_B23KGCJLT4_1\tLB:659_ezg-N1-BDNA-1_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.64 659_ezg-N1-BDNA-1_B23KGCJLT4_1_R1.fastq.gz 659_ezg-N1-BDNA-1_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 722.148 sec; CPU: 1670.172 sec
sorting block 0, #reads = 0 mem = 0 peak = 77205504
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: 37895
output reads: 0
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.024 user 0.116 sys 722.251 real
merge_files: 1 calls 0.009 user 0.094 sys 0.108 real
read_chunk: 2 calls 0.000 user 0.000 sys 0.002 real
sort_block: 1 calls 0.000 user 0.000 sys 0.002 real
overall: 262410240 mem 0.056 user 0.123 sys 722.274 real
ls: cannot access '*.cram': No such file or directory