cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_tumor.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 1064.669 CPU sec, 37.115 real sec
[M::process] read 124560 sequences (17940725 bp) in 0.157 CPU sec, 0.165 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 43403, 0, 7)
[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: (181, 272, 392)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 814)
[M::mem_pestat] mean and std.dev: (297.87, 148.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1025)
[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 124560 reads in 8.286 CPU sec, 0.280 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124560
overall: 68557361152 mem 1033.590 user 43.451 sys 41.490 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:REGRESSION.HCC1395_tumor.L004\tPU:L004\tSM:HCC1395_tumor\tLB:HCC1395_tumor\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 HCC1395_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 41.524 sec; CPU: 1077.043 sec
sorting block 0, #reads = 124723 mem = 59715543 peak = 168550400
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 96
algo: util-sort
license: sentieon:util=1
output file size: 7289742
output reads: 124723
bam_mem_sort: 1 calls 0.025 user 0.000 sys 0.028 real
bam_write: 1 calls 0.120 user 0.000 sys 0.117 real
execute: 1 calls 0.046 user 0.116 sys 41.925 real
merge_files: 1 calls 0.031 user 0.094 sys 0.242 real
parse_chunk: 2 calls 0.049 user 0.008 sys 0.072 real
read_chunk: 8 calls 0.044 user 0.019 sys 4.043 real
sort_block: 1 calls 0.193 user 0.020 sys 4.104 real
write_chunk: 4 calls 0.008 user 0.008 sys 0.026 real
overall: 498212864 mem 1.311 user 0.194 sys 41.943 real
ls: cannot access '*.cram': No such file or directory