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
[M::main_mem] bwa index loaded in 1722.154 CPU sec, 1026.656 real sec
[M::process] read 490 sequences (73416 bp) in 0.000 CPU sec, 0.001 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44, 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: (203, 293, 455)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 959)
[M::mem_pestat] mean and std.dev: (318.41, 138.19)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1211)
[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 490 reads in 0.600 CPU sec, 0.025 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: 490
overall: 68520316928 mem 1508.253 user 220.149 sys 1032.334 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.L006\tPU:L006\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: 1032.369 sec; CPU: 1728.404 sec
sorting block 0, #reads = 532 mem = 291979 peak = 75624448
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: 79368
output reads: 532
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.000 user 0.002 sys 0.003 real
execute: 1 calls 0.048 user 0.090 sys 1032.459 real
merge_files: 1 calls 0.038 user 0.062 sys 0.110 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
read_chunk: 4 calls 0.001 user 0.000 sys 5.653 real
sort_block: 1 calls 0.001 user 0.002 sys 5.653 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 264978432 mem 0.059 user 0.128 sys 1032.479 real
ls: cannot access '*.cram': No such file or directory