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: 50000139, nseq: 380326 [0000][ M::kt_pipeline] read 380326 sequences (50000139 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: 50000148, nseq: 381042 [0000][ M::kt_pipeline] read 381042 sequences (50000148 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 380326 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189165, 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: (169.10, 48.71) [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 380326 reads in 44.665 CPU sec, 11.023 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: 50000071, nseq: 382130 [0000][ M::kt_pipeline] read 382130 sequences (50000071 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 381042 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189142, 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, 170, 202) [0000][PE] low and high boundaries for computing mean and std.dev: (4, 334) [0000][PE] mean and std.dev: (169.51, 49.26) [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 381042 reads in 44.967 CPU sec, 11.115 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: 50000104, nseq: 382024 [0000][ M::kt_pipeline] read 382024 sequences (50000104 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 382130 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 190068, 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: (168.42, 49.72) [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 382130 reads in 44.121 CPU sec, 10.880 real sec [0000] Calling mem_process_seqs.., task: 3 [0000] 1. Calling kt_for - worker_bwt [0000] read_chunk: 50000000, work_chunk_size: 29717809, nseq: 226420 [0000][ M::kt_pipeline] read 226420 sequences (29717809 bp)... [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 3209286105, n: 382024 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 189753, 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, 201) [0000][PE] low and high boundaries for computing mean and std.dev: (3, 333) [0000][PE] mean and std.dev: (168.22, 49.27) [0000][PE] low and high boundaries for proper pairs: (1, 399) [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 382024 reads in 44.370 CPU sec, 11.004 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: 226420 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 112442, 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: (168.92, 48.89) [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 226420 reads in 25.795 CPU sec, 6.432 real sec [0000] read_chunk: 50000000, work_chunk_size: 0, nseq: 0 [0000] Computation ends.. No. of OMP threads: 4 Processor is running @3000.484954 MHz Runtime profile: Time taken for main_mem function: 62.15 sec IO times (sec) : Reading IO time (reads) avg: 3.08, (3.08, 3.08) Writing IO time (SAM) avg: 1.06, (1.06, 1.06) Reading IO time (Reference Genome) avg: 3.89, (3.89, 3.89) Index read time avg: 6.09, (6.09, 6.09) Overall time (sec) (Excluding Index reading time): PROCESS() (Total compute time + (read + SAM) IO time) : 51.42 MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 50.45, (50.45, 50.45) SAM Processing time (sec): --WORKER_SAM avg: 16.20, (16.20, 16.20) Kernels' compute time (sec): Total kernel (smem+sal+bsw) time avg: 34.05, (34.05, 34.05) SMEM compute avg: 21.92, (21.95, 21.89) SAL compute avg: 2.76, (2.76, 2.75) MEM_SA avg: 1.67, (1.68, 1.66) BSW time, avg: 8.78, (8.79, 8.77) 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...