cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o 659_Lx-T1-TDNA-1_A23MHWWLT4_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
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 2701.640 CPU sec, 111.939 real sec
[M::process] read 65384 sequences (8965433 bp) in 0.086 CPU sec, 0.088 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 24881, 10, 3)
[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: (129, 179, 255)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 507)
[M::mem_pestat] mean and std.dev: (198.33, 92.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 633)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1089, 1115, 1138)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (991, 1236)
[M::mem_pestat] mean and std.dev: (1110.43, 20.49)
[M::mem_pestat] low and high boundaries for proper pairs: (942, 1285)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 65384 reads in 32.846 CPU sec, 1.083 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: 65384
overall: 68010676224 mem 2206.123 user 536.297 sys 120.958 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:A23MHWWLT4.659_Lx-T1-TDNA-1_A23MHWWLT4_1.L004\tPU:L004\tSM:659_Lx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_Lx-T1-TDNA-1_A23MHWWLT4_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_Lx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_Lx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 120.991 sec; CPU: 2742.424 sec
sorting block 0, #reads = 66034 mem = 32596076 peak = 129040384
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 384
algo: util-sort
license: sentieon:util=1
output file size: 5051557
output reads: 66034
bam_mem_sort: 1 calls 0.019 user 0.000 sys 0.023 real
bam_write: 1 calls 0.023 user 0.004 sys 0.023 real
execute: 1 calls 0.055 user 0.143 sys 121.317 real
merge_files: 1 calls 0.042 user 0.106 sys 0.241 real
parse_chunk: 1 calls 0.027 user 0.027 sys 0.055 real
read_chunk: 5 calls 0.004 user 0.046 sys 7.934 real
sort_block: 1 calls 0.060 user 0.072 sys 7.946 real
write_chunk: 2 calls 0.000 user 0.019 sys 0.023 real
overall: 320925696 mem 1.006 user 0.314 sys 121.337 real
ls: cannot access '*.cram': No such file or directory