Looking to launch executable "/opt/conda/bin/bwa-meme_mode2.avx2", simd = _mode2.avx2 Launching executable "/opt/conda/bin/bwa-meme_mode2.avx2" ----------------------------- Executing in AVX2 mode!! ----------------------------- * SA compression enabled with xfactor: 8 * Ref file: reference.902362185.genome.fasta * Entering FMI_search Reading other elements of the index from files reference.902362185.genome.fasta * Index prefix: reference.902362185.genome.fasta * Read 0 ALT contigs * Reading reference genome.. * Binary seq file = reference.902362185.genome.fasta.0123 * Reference genome size: 1312223304 bp * Done reading reference genome !! ------------------------------------------ 1. Memory pre-allocation for Chaining: 4543.5970 MB 2. Memory pre-allocation for BSW: 7667.7448 MB [M::memoryAllocLearned::MEME] Reading Learned-index models into memory [Learned-Config] MODE:2 SEARCH_METHOD: 1 MEM_TRADEOFF:0 EXPONENTIAL_SMEMSEARCH: 1 DEBUG_MODE:0 Num 2nd Models:268435456 PWL Bits Used:28 [M::memoryAllocLearned::MEME] Loading RMI model and Pac reference file took 63.078 sec [M::memoryAllocLearned::MEME] Reading suffix array into memory [M::memoryAllocLearned::MEME] Loading pos_packed file took 131.611 sec [M::memoryAllocLearned::MEME] Generating SA and 64-bit Suffix in memory [M::memoryAllocLearned::MEME] Runtime-build-index took 8.144 sec 3. Memory pre-allocation for BWT: 17573.6155 MB ------------------------------------------ * Threads used (compute): 32 * No. of pipeline threads: 2 [0000] read_chunk: 320000000, work_chunk_size: 320000241, nseq: 2213524 [0000][ M::kt_pipeline] read 2213524 sequences (320000241 bp)... [0000] Reallocating initial memory allocations!! [0000] Calling mem_process_seqs.., task: 0 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2213524 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (72, 878173, 99, 54) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (140, 199, 259) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 497) [0000][PE] mean and std.dev: (176.72, 69.23) [0000][PE] low and high boundaries for proper pairs: (1, 616) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.89, 60.99) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (247, 1320, 5768) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 16810) [0000][PE] mean and std.dev: (2997.02, 3222.90) [0000][PE] low and high boundaries for proper pairs: (1, 22331) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (116, 181, 277) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 599) [0000][PE] mean and std.dev: (170.60, 84.89) [0000][PE] low and high boundaries for proper pairs: (1, 760) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 320000104, nseq: 2215146 [0000][ M::kt_pipeline] read 2215146 sequences (320000104 bp)... [0000][ M::mem_process_seqs] Processed 2213524 reads in 411.932 CPU sec, 13.429 real sec [0000] Reallocating initial memory allocations!! [0000] Calling mem_process_seqs.., task: 1 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2215146 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (86, 901591, 82, 77) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (125, 202, 295) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 635) [0000][PE] mean and std.dev: (177.76, 78.20) [0000][PE] low and high boundaries for proper pairs: (1, 805) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.81, 61.06) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (529, 2234, 6456) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 18310) [0000][PE] mean and std.dev: (3601.27, 3289.97) [0000][PE] low and high boundaries for proper pairs: (1, 24237) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (163, 218, 2447) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 7015) [0000][PE] mean and std.dev: (1429.29, 2269.84) [0000][PE] low and high boundaries for proper pairs: (1, 10509) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 320000043, nseq: 2214912 [0000][ M::kt_pipeline] read 2214912 sequences (320000043 bp)... [0000][ M::mem_process_seqs] Processed 2215146 reads in 335.010 CPU sec, 11.194 real sec [0000] Calling mem_process_seqs.., task: 2 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2214912 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (72, 896804, 96, 64) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (141, 219, 720) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1878) [0000][PE] mean and std.dev: (347.56, 411.28) [0000][PE] low and high boundaries for proper pairs: (1, 2457) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.82, 61.06) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (730, 3009, 7690) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 21610) [0000][PE] mean and std.dev: (3891.67, 3335.95) [0000][PE] low and high boundaries for proper pairs: (1, 28570) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (131, 173, 233) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 437) [0000][PE] mean and std.dev: (162.12, 62.19) [0000][PE] low and high boundaries for proper pairs: (1, 539) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000][ M::mem_process_seqs] Processed 2214912 reads in 353.457 CPU sec, 11.776 real sec [0000] read_chunk: 320000000, work_chunk_size: 320000176, nseq: 2212746 [0000][ M::kt_pipeline] read 2212746 sequences (320000176 bp)... [0000] Calling mem_process_seqs.., task: 3 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2212746 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (81, 874704, 98, 80) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (152, 210, 622) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1562) [0000][PE] mean and std.dev: (314.36, 340.02) [0000][PE] low and high boundaries for proper pairs: (1, 2032) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.81, 60.95) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (809, 2140, 6056) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 16550) [0000][PE] mean and std.dev: (3615.13, 3078.10) [0000][PE] low and high boundaries for proper pairs: (1, 21797) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (153, 222, 261) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 477) [0000][PE] mean and std.dev: (190.40, 72.32) [0000][PE] low and high boundaries for proper pairs: (1, 585) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 320000068, nseq: 2214044 [0000][ M::kt_pipeline] read 2214044 sequences (320000068 bp)... [0000][ M::mem_process_seqs] Processed 2212746 reads in 427.522 CPU sec, 14.089 real sec [0000] Calling mem_process_seqs.., task: 4 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2214044 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (68, 890084, 86, 53) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (142, 196, 276) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 544) [0000][PE] mean and std.dev: (182.50, 89.41) [0000][PE] low and high boundaries for proper pairs: (1, 678) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.99, 60.93) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (647, 2579, 6731) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 18899) [0000][PE] mean and std.dev: (3797.67, 3507.26) [0000][PE] low and high boundaries for proper pairs: (1, 24983) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (152, 226, 981) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 2639) [0000][PE] mean and std.dev: (322.77, 469.58) [0000][PE] low and high boundaries for proper pairs: (1, 3468) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 320000192, nseq: 2213126 [0000][ M::kt_pipeline] read 2213126 sequences (320000192 bp)... [0000][ M::mem_process_seqs] Processed 2214044 reads in 389.160 CPU sec, 13.067 real sec [0000] Calling mem_process_seqs.., task: 5 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2213126 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (86, 888524, 120, 62) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (157, 233, 1544) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 4318) [0000][PE] mean and std.dev: (626.71, 979.06) [0000][PE] low and high boundaries for proper pairs: (1, 5705) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.91, 61.00) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (780, 3044, 7316) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 20388) [0000][PE] mean and std.dev: (3867.18, 3282.78) [0000][PE] low and high boundaries for proper pairs: (1, 26924) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (135, 200, 464) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1122) [0000][PE] mean and std.dev: (190.27, 106.19) [0000][PE] low and high boundaries for proper pairs: (1, 1451) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 320000159, nseq: 2214724 [0000][ M::kt_pipeline] read 2214724 sequences (320000159 bp)... [0000][ M::mem_process_seqs] Processed 2213126 reads in 380.853 CPU sec, 13.080 real sec [0000] Calling mem_process_seqs.., task: 6 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2214724 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (71, 898717, 105, 65) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (144, 202, 299) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 609) [0000][PE] mean and std.dev: (186.70, 91.90) [0000][PE] low and high boundaries for proper pairs: (1, 764) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.87, 61.03) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (727, 3285, 5865) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 16141) [0000][PE] mean and std.dev: (3620.79, 3087.55) [0000][PE] low and high boundaries for proper pairs: (1, 21279) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (162, 210, 528) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1260) [0000][PE] mean and std.dev: (255.52, 201.38) [0000][PE] low and high boundaries for proper pairs: (1, 1626) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000][ M::mem_process_seqs] Processed 2214724 reads in 344.213 CPU sec, 11.598 real sec [0000] read_chunk: 320000000, work_chunk_size: 320000112, nseq: 2214752 [0000][ M::kt_pipeline] read 2214752 sequences (320000112 bp)... [0000] Calling mem_process_seqs.., task: 7 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2214752 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (47, 895728, 118, 65) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (154, 198, 526) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1270) [0000][PE] mean and std.dev: (244.46, 218.16) [0000][PE] low and high boundaries for proper pairs: (1, 1642) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.82, 61.05) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (758, 3525, 6540) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 18104) [0000][PE] mean and std.dev: (3765.44, 3141.51) [0000][PE] low and high boundaries for proper pairs: (1, 23886) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (162, 217, 622) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1542) [0000][PE] mean and std.dev: (257.74, 179.93) [0000][PE] low and high boundaries for proper pairs: (1, 2002) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 320000190, nseq: 2213640 [0000][ M::kt_pipeline] read 2213640 sequences (320000190 bp)... [0000][ M::mem_process_seqs] Processed 2214752 reads in 357.981 CPU sec, 11.875 real sec [0000] Calling mem_process_seqs.., task: 8 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2213640 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (69, 888845, 75, 47) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (143, 196, 270) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 524) [0000][PE] mean and std.dev: (184.69, 73.09) [0000][PE] low and high boundaries for proper pairs: (1, 651) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.85, 60.97) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (712, 2253, 5709) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 15703) [0000][PE] mean and std.dev: (3350.47, 2946.76) [0000][PE] low and high boundaries for proper pairs: (1, 20700) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (150, 186, 264) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 492) [0000][PE] mean and std.dev: (179.35, 77.57) [0000][PE] low and high boundaries for proper pairs: (1, 606) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000][ M::mem_process_seqs] Processed 2213640 reads in 394.317 CPU sec, 13.450 real sec [0000] read_chunk: 320000000, work_chunk_size: 320000293, nseq: 2214746 [0000][ M::kt_pipeline] read 2214746 sequences (320000293 bp)... [0000] Calling mem_process_seqs.., task: 9 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2214746 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (81, 902616, 105, 63) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (137, 197, 260) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 506) [0000][PE] mean and std.dev: (178.85, 77.75) [0000][PE] low and high boundaries for proper pairs: (1, 629) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 287, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.87, 61.00) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (952, 4551, 7455) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 20461) [0000][PE] mean and std.dev: (4416.41, 3308.48) [0000][PE] low and high boundaries for proper pairs: (1, 26964) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (154, 183, 249) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 439) [0000][PE] mean and std.dev: (171.15, 56.82) [0000][PE] low and high boundaries for proper pairs: (1, 534) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000] read_chunk: 320000000, work_chunk_size: 292093224, nseq: 2021886 [0000][ M::kt_pipeline] read 2021886 sequences (292093224 bp)... [0000][ M::mem_process_seqs] Processed 2214746 reads in 335.927 CPU sec, 11.222 real sec [0000] Calling mem_process_seqs.., task: 10 [0000] 1. Calling kt_for - worker_bwt [0000] 2. Calling kt_for - worker_aln [0000] read_chunk: 320000000, work_chunk_size: 0, nseq: 0 [0000] Inferring insert size distribution of PE reads from data, l_pac: 656111652, n: 2021886 [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (70, 821230, 85, 40) [0000][PE] analyzing insert size distribution for orientation FF... [0000][PE] (25, 50, 75) percentile: (142, 201, 708) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1840) [0000][PE] mean and std.dev: (318.48, 343.46) [0000][PE] low and high boundaries for proper pairs: (1, 2406) [0000][PE] analyzing insert size distribution for orientation FR... [0000][PE] (25, 50, 75) percentile: (244, 286, 325) [0000][PE] low and high boundaries for computing mean and std.dev: (82, 487) [0000][PE] mean and std.dev: (280.70, 61.01) [0000][PE] low and high boundaries for proper pairs: (1, 568) [0000][PE] analyzing insert size distribution for orientation RF... [0000][PE] (25, 50, 75) percentile: (194, 837, 4265) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 12407) [0000][PE] mean and std.dev: (2320.80, 2755.53) [0000][PE] low and high boundaries for proper pairs: (1, 16478) [0000][PE] analyzing insert size distribution for orientation RR... [0000][PE] (25, 50, 75) percentile: (166, 224, 505) [0000][PE] low and high boundaries for computing mean and std.dev: (1, 1183) [0000][PE] mean and std.dev: (223.06, 140.24) [0000][PE] low and high boundaries for proper pairs: (1, 1522) [0000][PE] skip orientation FF [0000][PE] skip orientation RF [0000][PE] skip orientation RR [0000] 3. Calling kt_for - worker_sam [0000][ M::mem_process_seqs] Processed 2021886 reads in 323.166 CPU sec, 10.899 real sec [0000] read_chunk: 320000000, work_chunk_size: 0, nseq: 0 [0000] Computation ends.. No. of OMP threads: 32 Processor is running @2297.593619 MHz Runtime profile: Time taken for main_mem function: 303.28 sec IO times (sec) : Reading IO time (reads) avg: 104.64, (104.64, 104.64) Writing IO time (SAM) avg: 26.54, (26.54, 26.54) Reading IO time (Reference Genome) avg: 11.82, (11.82, 11.82) Index read time avg: 1.49, (1.49, 1.49) Overall time (sec) (Excluding Index reading time): PROCESS() (Total compute time + (read + SAM) IO time) : 289.96 MEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 135.67, (135.67, 135.67) SAM Processing time (sec): --WORKER_SAM avg: 60.57, (60.57, 60.57) Kernels' compute time (sec): Total kernel (smem+sal+bsw) time avg: 73.45, (73.45, 73.45) MEM_ALN_CHAIN_FLT avg: 0.00, (0.00, 0.00) MEM_ALN_CHAIN_SEED avg: 0.00, (0.00, 0.00) ERT_SEED_CHAIN avg: 0.00, (0.00, 0.00) LEARNED_SEED_CHAIN avg: 19.37, (19.41, 19.28) SMEM compute avg: 0.00, (0.00, 0.00) SAL compute avg: 0.00, (0.00, 0.00) MEM_SA avg: 0.00, (0.00, 0.00) BSW time, avg: 51.31, (52.06, 51.03) 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: 32 SIMD_WIDTH16 X: 16 AVG_SEEDS_PER_READ: 64