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: 50000046, nseq: 380766 [0000][ M::kt_pipeline] read 380766 sequences (50000046 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: 50000129, nseq: 380614 [0000][ M::kt_pipeline] read 380614 sequences (50000129 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380766 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189210, 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, 202) [0000][PE] low and high boundaries for computing mean and std.dev: (4, 334) [0000][PE] mean and std.dev: (169.40, 49.13) [0000][PE] low and high boundaries for proper pairs: (1, 400) [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 380766 reads in 45.108 CPU sec, 11.145 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: 50000090, nseq: 381478 [0000][ M::kt_pipeline] read 381478 sequences (50000090 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380614 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189158, 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: (169.16, 48.87) [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 380614 reads in 45.059 CPU sec, 11.123 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: 50000276, nseq: 381594 [0000][ M::kt_pipeline] read 381594 sequences (50000276 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381478 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189649, 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: (169.35, 49.72) [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 381478 reads in 44.656 CPU sec, 11.002 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: 29809520, nseq: 227414 [0000][ M::kt_pipeline] read 227414 sequences (29809520 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381594 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189618, 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: (168.71, 49.20) [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 381594 reads in 45.112 CPU sec, 11.190 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: 227414 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 113083, 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, 168, 202) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 336) [0000][PE] mean and std.dev: (168.71, 49.53) [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 227414 reads in 26.611 CPU sec, 6.658 real sec [0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0 [0000] Computation ends.. No. of OMP threads: 4 Processor is running @3000.208338 MHz Runtime profile: Time taken for main_mem function: 62.82 sec IO times (sec) : Reading IO time (reads) avg: 3.17, (3.17, 3.17) Writing IO time (SAM) avg: 1.09, (1.09, 1.09) Reading IO time (Reference Genome) avg: 3.87, (3.87, 3.87) Index read time avg: 6.12, (6.12, 6.12) Overall time (sec) (Excluding Index reading time): PROCESS() (Total compute time + (read + SAM) IO time) : 52.12 MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 51.12, (51.12, 51.12) SAM Processing time (sec): --WORKER_SAM avg: 16.18, (16.18, 16.18) Kernels' compute time (sec): Total kernel (smem+sal+bsw) time avg: 34.73, (34.73, 34.73) SMEM compute avg: 22.09, (22.13, 22.07) SAL compute avg: 2.87, (2.88, 2.86) MEM_SA avg: 1.73, (1.73, 1.72) BSW time, avg: 9.09, (9.11, 9.09) 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...