Looking to launch executable "/opt/conda/bin/bwa-mem2.avx512bw", simd = .avx512bw
Launching executable "/opt/conda/bin/bwa-mem2.avx512bw"
-----------------------------
Executing in AVX512 mode!!
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* SA compression enabled with xfactor: 8
* Ref file: hg38.fa
* Entering FMI_search
* Index file found. Loading index from hg38.fa.bwt.2bit.64
* Reference seq len for bi-index = 6418572211
* sentinel-index: 2729492284
* Count:
0, 1
1, 1879238230
2, 3209286106
3, 4539333982
4, 6418572211
* Reading other elements of the index from files hg38.fa
* Index prefix: hg38.fa
* Read 0 ALT contigs
* Done reading Index!!
* Reading reference genome..
* Binary seq file = hg38.fa.0123
* Reference genome size: 6418572210 bp
* Done reading reference genome !!
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1. Memory pre-allocation for Chaining: 696.7080 MB
2. Memory pre-allocation for BSW: 1437.7021 MB
3. Memory pre-allocation for BWT: 463.8851 MB
------------------------------------------
* Threads used (compute): 6
* No. of pipeline threads: 2
[0000] read_chunk: 50000000, work_chunk_size: 50000004, nseq: 360792
[0000][ M::kt_pipeline] read 360792 sequences (50000004 bp)...
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 0
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 18252405, nseq: 131638
[0000][ M::kt_pipeline] read 131638 sequences (18252405 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 360792
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (15, 150576, 69, 0)
[0000][PE] analyzing insert size distribution for orientation FF...
[0000][PE] (25, 50, 75) percentile: (279, 1168, 1799)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 4839)
[0000][PE] mean and std.dev: (716.83, 655.81)
[0000][PE] low and high boundaries for proper pairs: (1, 6359)
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (242, 329, 429)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 803)
[0000][PE] mean and std.dev: (340.98, 140.06)
[0000][PE] low and high boundaries for proper pairs: (1, 990)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (17, 33, 129)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 353)
[0000][PE] mean and std.dev: (59.36, 55.50)
[0000][PE] low and high boundaries for proper pairs: (1, 465)
[0000][PE] skip orientation RR as there are not enough pairs
[0000][PE] skip orientation FF
[0000][PE] skip orientation RF
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 360792 reads in 94.961 CPU sec, 15.883 real sec
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 131638
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (3, 55027, 13, 2)
[0000][PE] skip orientation FF as there are not enough pairs
[0000][PE] analyzing insert size distribution for orientation FR...
[0000][PE] (25, 50, 75) percentile: (242, 330, 431)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 809)
[0000][PE] mean and std.dev: (343.14, 142.88)
[0000][PE] low and high boundaries for proper pairs: (1, 998)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (33, 77, 90)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 204)
[0000][PE] mean and std.dev: (62.23, 30.14)
[0000][PE] low and high boundaries for proper pairs: (1, 261)
[0000][PE] skip orientation RR as there are not enough pairs
[0000][PE] skip orientation RF
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 131638 reads in 32.898 CPU sec, 5.524 real sec
[0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 6
Processor is running @2500.151460 MHz
Runtime profile:
Time taken for main_mem function: 33.21 sec
IO times (sec) :
Reading IO time (reads) avg: 1.09, (1.09, 1.09)
Writing IO time (SAM) avg: 0.58, (0.58, 0.58)
Reading IO time (Reference Genome) avg: 3.66, (3.66, 3.66)
Index read time avg: 6.46, (6.46, 6.46)
Overall time (sec) (Excluding Index reading time):
PROCESS() (Total compute time + (read + SAM) IO time) : 22.32
MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 21.41, (21.41, 21.41)
SAM Processing time (sec):
--WORKER_SAM avg: 7.30, (7.30, 7.30)
Kernels' compute time (sec):
Total kernel (smem+sal+bsw) time avg: 14.05, (14.05, 14.05)
SMEM compute avg: 5.95, (6.26, 5.61)
SAL compute avg: 2.07, (2.13, 2.00)
MEM_SA avg: 1.16, (1.20, 1.13)
BSW time, avg: 4.40, (4.42, 4.37)
Important parameter settings:
BATCH_SIZE: 512
MAX_SEQ_LEN_REF: 256
MAX_SEQ_LEN_QER: 128
MAX_SEQ_LEN8: 128
SEEDS_PER_READ: 500
SIMD_WIDTH8 X: 64
SIMD_WIDTH16 X: 32
AVG_SEEDS_PER_READ: 64
[bam_sort_core] merging from 0 files and 6 in-memory blocks...