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: 958.4681 MB
3. Memory pre-allocation for BWT: 309.2567 MB
------------------------------------------
* Threads used (compute): 4
* No. of pipeline threads: 2
[0000] read_chunk: 50000000, work_chunk_size: 50000224, nseq: 380990
[0000][ M::kt_pipeline] read 380990 sequences (50000224 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: 50000039, nseq: 381094
[0000][ M::kt_pipeline] read 381094 sequences (50000039 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380990
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189493, 0, 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: (135, 169, 203)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 339)
[0000][PE] mean and std.dev: (168.85, 49.14)
[0000][PE] low and high boundaries for proper pairs: (1, 407)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 380990 reads in 32.050 CPU sec, 7.937 real sec
[0000] Reallocating initial memory allocations!!
[W::sam_hrecs_update_hashes] PG line with multiple ID tags. The first encountered was preferred - ID:bwa-mem2
[0000] Calling mem_process_seqs.., task: 1
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 50000276, nseq: 381426
[0000][ M::kt_pipeline] read 381426 sequences (50000276 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381094
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189660, 0, 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: (134, 169, 202)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 338)
[0000][PE] mean and std.dev: (168.88, 49.53)
[0000][PE] low and high boundaries for proper pairs: (1, 406)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 381094 reads in 32.905 CPU sec, 8.080 real sec
[0000] Reallocating initial memory allocations!!
[0000] Calling mem_process_seqs.., task: 2
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 50000158, nseq: 380668
[0000][ M::kt_pipeline] read 380668 sequences (50000158 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381426
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189868, 0, 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: (134, 168, 202)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 338)
[0000][PE] mean and std.dev: (168.43, 49.30)
[0000][PE] low and high boundaries for proper pairs: (1, 406)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 381426 reads in 32.254 CPU sec, 7.969 real sec
[0000] Calling mem_process_seqs.., task: 3
[0000] 1. Calling kt_for - worker_bwt
[0000] read_chunk: 50000000, work_chunk_size: 28728407, nseq: 219430
[0000][ M::kt_pipeline] read 219430 sequences (28728407 bp)...
[0000] 2. Calling kt_for - worker_aln
[0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380668
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189299, 0, 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: (136, 169, 203)
[0000][PE] low and high boundaries for computing mean and std.dev: (2, 337)
[0000][PE] mean and std.dev: (169.57, 49.50)
[0000][PE] low and high boundaries for proper pairs: (1, 404)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 380668 reads in 31.881 CPU sec, 7.909 real sec
[0000] Calling mem_process_seqs.., task: 4
[0000] 1. Calling kt_for - worker_bwt
[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: 219430
[0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 109171, 0, 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: (134, 168, 201)
[0000][PE] low and high boundaries for computing mean and std.dev: (1, 335)
[0000][PE] mean and std.dev: (167.89, 49.18)
[0000][PE] low and high boundaries for proper pairs: (1, 402)
[0000][PE] skip orientation RF as there are not enough pairs
[0000][PE] skip orientation RR as there are not enough pairs
[0000] 3. Calling kt_for - worker_sam
[0000][ M::mem_process_seqs] Processed 219430 reads in 17.607 CPU sec, 4.393 real sec
[0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0
[0000] Computation ends..
No. of OMP threads: 4
Processor is running @2700.238122 MHz
Runtime profile:
Time taken for main_mem function: 45.09 sec
IO times (sec) :
Reading IO time (reads) avg: 2.92, (2.92, 2.92)
Writing IO time (SAM) avg: 1.11, (1.11, 1.11)
Reading IO time (Reference Genome) avg: 3.00, (3.00, 3.00)
Index read time avg: 4.44, (4.44, 4.44)
Overall time (sec) (Excluding Index reading time):
PROCESS() (Total compute time + (read + SAM) IO time) : 37.23
MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 36.28, (36.28, 36.28)
SAM Processing time (sec):
--WORKER_SAM avg: 7.44, (7.44, 7.44)
Kernels' compute time (sec):
Total kernel (smem+sal+bsw) time avg: 28.67, (28.67, 28.67)
SMEM compute avg: 19.79, (19.80, 19.78)
SAL compute avg: 2.20, (2.22, 2.19)
MEM_SA avg: 1.43, (1.44, 1.41)
BSW time, avg: 6.25, (6.25, 6.24)
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 4 in-memory blocks...