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: 50000154, nseq: 379600 [0000][ M::kt_pipeline] read 379600 sequences (50000154 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: 50000038, nseq: 379768 [0000][ M::kt_pipeline] read 379768 sequences (50000038 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 379600 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 188812, 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: (137, 169, 202) [0000][PE] low and high boundaries for computing mean and std.dev: (7, 332) [0000][PE] mean and std.dev: (169.59, 48.59) [0000][PE] low and high boundaries for proper pairs: (1, 397) [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 379600 reads in 30.722 CPU sec, 7.606 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: 50000096, nseq: 380632 [0000][ M::kt_pipeline] read 380632 sequences (50000096 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 379768 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 188899, 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: (169.56, 48.50) [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 379768 reads in 32.415 CPU sec, 7.963 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: 50000080, nseq: 381286 [0000][ M::kt_pipeline] read 381286 sequences (50000080 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380632 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189221, 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, 202) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 336) [0000][PE] mean and std.dev: (169.02, 48.67) [0000][PE] low and high boundaries for proper pairs: (1, 403) [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 380632 reads in 33.856 CPU sec, 8.310 real sec [0000] Reallocating initial memory allocations!! [0000] Calling mem_process_seqs.., task: 3 [0000] 1. Calling kt_for - worker_bwt [0000] read_chunk: 50000000, work_chunk_size: 31334196, nseq: 238858 [0000][ M::kt_pipeline] read 238858 sequences (31334196 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381286 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189301, 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, 167, 202) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 336) [0000][PE] mean and std.dev: (168.63, 49.15) [0000][PE] low and high boundaries for proper pairs: (1, 403) [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 381286 reads in 32.896 CPU sec, 8.144 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: 238858 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 118632, 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, 170, 204) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 342) [0000][PE] mean and std.dev: (169.94, 49.54) [0000][PE] low and high boundaries for proper pairs: (1, 411) [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 238858 reads in 19.937 CPU sec, 4.973 real sec [0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0 [0000] Computation ends.. No. of OMP threads: 4 Processor is running @2700.246754 MHz Runtime profile: Time taken for main_mem function: 45.74 sec IO times (sec) : Reading IO time (reads) avg: 2.99, (2.99, 2.99) Writing IO time (SAM) avg: 1.13, (1.13, 1.13) Reading IO time (Reference Genome) avg: 2.95, (2.95, 2.95) Index read time avg: 4.42, (4.42, 4.42) Overall time (sec) (Excluding Index reading time): PROCESS() (Total compute time + (read + SAM) IO time) : 37.95 MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 36.99, (36.99, 36.99) SAM Processing time (sec): --WORKER_SAM avg: 7.81, (7.81, 7.81) Kernels' compute time (sec): Total kernel (smem+sal+bsw) time avg: 29.04, (29.04, 29.04) SMEM compute avg: 20.06, (20.07, 20.04) SAL compute avg: 2.24, (2.25, 2.23) MEM_SA avg: 1.43, (1.45, 1.42) BSW time, avg: 6.30, (6.31, 6.30) 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...