RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.F779UU/RM_31370.SunDec30437362023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1701607055 Database = /dev/shm/rModeler.F779UU/GCA_030490855.1_bPoeAtr1.hap2 - Sequences = 157 - Bases = 987998379 - N50 = 117237321 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 168859252-180920413 | [ 1 ] 156798091-168859251 | [ ] 144736930-156798090 | [ 1 ] 132675769-144736929 | [ ] 120614608-132675768 | [ ] 108553447-120614607 | [ 1 ] 96492286-108553446 | [ ] 84431126-96492286 | [ ] 72369965-84431125 | [ 1 ] 60308804-72369964 | [ ] 48247643-60308803 | [ ] 36186482-48247642 | [ 2 ] 24125321-36186481 |* [ 3 ] 12064160-24125320 |** [ 8 ] 3000-12064160 |************************************************** [ 140 ] Storage Throughput = excellent ( 1086.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40053033 bp ( 40019848 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:04 (hh:mm:ss) Elapsed Time Round Time: 00:31:20 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2296 repeats masked totaling 645943 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002302 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10001902 bp After Masking: 8930393 bp Masked: 10.71 % -- Input Database Coverage: 10002302 bp out of 987998379 bp ( 1.01 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:47 (hh:mm:ss) Elapsed Time, 14662 HSPs Collected Number of families returned by RECON: 297 Round Time: 00:08:22 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8407 repeats masked totaling 2205734 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30050651 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30017866 bp After Masking: 26965687 bp Masked: 10.17 % -- Input Database Coverage: 40052953 bp out of 987998379 bp ( 4.05 % ) Sampling Time: 00:04:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:48:59 (hh:mm:ss) Elapsed Time, 32444 HSPs Collected Number of families returned by RECON: 1701 Round Time: 00:55:07 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36316 repeats masked totaling 8050199 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90076209 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 90015310 bp After Masking: 79406224 bp Masked: 11.79 % -- Input Database Coverage: 130129162 bp out of 987998379 bp ( 13.17 % ) Sampling Time: 00:11:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 05:34:18 (hh:mm:ss) Elapsed Time, 1013444 HSPs Collected Number of families returned by RECON: 10039 Round Time: 05:51:06 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124892 repeats masked totaling 30603771 bp(s). - TE Masking time 00:05:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270195314 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 270024039 bp After Masking: 231568656 bp Masked: 14.24 % -- Input Database Coverage: 400324476 bp out of 987998379 bp ( 40.52 % ) Sampling Time: 00:38:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 42:48:55 (hh:mm:ss) Elapsed Time, 6722563 HSPs Collected Number of families returned by RECON: 68762 Round Time: 44:54:53 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatScout/RECON discovery complete: 522 families found Classification Time: 01:07:19 (hh:mm:ss) Elapsed Time Program Time: 53:28:07 (hh:mm:ss) Elapsed Time