Looking to launch executable "/opt/conda/bin/bwa-mem2.avx512bw", simd = .avx512bw
Launching executable "/opt/conda/bin/bwa-mem2.avx512bw"
-----------------------------
Executing in AVX512 mode!!
-----------------------------
* 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 !!

------------------------------------------
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: 50000067, nseq: 360124
	[0000][ M::kt_pipeline] read 360124 sequences (50000067 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: 18456421, nseq: 132822
	[0000][ M::kt_pipeline] read 132822 sequences (18456421 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 360124
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (4, 151655, 47, 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: (221, 303, 387)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 719)
[0000][PE] mean and std.dev: (311.76, 122.51)
[0000][PE] low and high boundaries for proper pairs: (1, 885)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (37, 71, 123)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 295)
[0000][PE] mean and std.dev: (77.30, 51.39)
[0000][PE] low and high boundaries for proper pairs: (1, 381)
[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 360124 reads in 63.436 CPU sec, 10.684 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: 132822
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 55741, 28, 0)
[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: (223, 305, 391)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 727)
[0000][PE] mean and std.dev: (315.09, 123.87)
[0000][PE] low and high boundaries for proper pairs: (1, 895)
[0000][PE] analyzing insert size distribution for orientation RF...
[0000][PE] (25, 50, 75) percentile: (29, 66, 140)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 362)
[0000][PE] mean and std.dev: (83.96, 60.56)
[0000][PE] low and high boundaries for proper pairs: (1, 473)
[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 132822 reads in 22.447 CPU sec, 3.762 real sec
[0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 6
Processor is running @2700.210808 MHz
Runtime profile:

	Time taken for main_mem function: 22.62 sec

	IO times (sec) :
	Reading IO time (reads) avg: 0.71, (0.71, 0.71)
	Writing IO time (SAM) avg: 0.31, (0.31, 0.31)
	Reading IO time (Reference Genome) avg: 2.64, (2.64, 2.64)
	Index read time avg: 4.53, (4.53, 4.53)

	Overall time (sec) (Excluding Index reading time):
	PROCESS() (Total compute time + (read + SAM) IO time) : 15.06
	MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 14.45, (14.45, 14.45)

	 SAM Processing time (sec):
	--WORKER_SAM avg: 3.35, (3.35, 3.35)

	Kernels' compute time (sec):
	Total kernel (smem+sal+bsw) time avg: 11.04, (11.04, 11.04)
		SMEM compute avg: 6.79, (7.02, 6.67)
		SAL compute avg: 1.55, (1.60, 1.47)
				MEM_SA avg: 0.99, (1.02, 0.93)

		BSW time, avg: 1.98, (1.99, 1.97)

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...