RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.GlEz4L/RM_3801448.TueNov191634592024 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: 1732062898 Database = /scratch/tmp/rModeler.GlEz4L/GCA_040206685.1_aAscTru1.hap1 - Sequences = 3549 - Bases = 3722616900 - N50 = 439620316 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 518768054-555822420 | [ 1 ] 481713688-518768053 | [ 1 ] 444659322-481713687 | [ ] 407604956-444659321 | [ 2 ] 370550590-407604955 | [ ] 333496224-370550589 | [ ] 296441858-333496223 | [ 1 ] 259387492-296441857 | [ ] 222333126-259387491 | [ ] 185278760-222333125 | [ ] 148224394-185278759 | [ ] 111170028-148224393 | [ 2 ] 74115662-111170027 | [ 1 ] 37061296-74115661 | [ 11 ] 6931-37061296 |************************************************** [ 3530 ] Storage Throughput = excellent ( 1634.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042362 bp ( 40026962 non ambiguous ) - Num Contigs Represented = 155 - Sequence extraction : 00:02:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:21 (hh:mm:ss) Elapsed Time Round Time: 00:21:22 (hh:mm:ss) Elapsed Time : 1078 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15578 repeats masked totaling 4432657 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007584 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10004584 bp After Masking: 3749729 bp Masked: 62.52 % -- Input Database Coverage: 10007584 bp out of 3722616900 bp ( 0.27 % ) Sampling Time: 00:05:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:47 (hh:mm:ss) Elapsed Time, 8579 HSPs Collected Number of families returned by RECON: 1257 Round Time: 00:08:52 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49575 repeats masked totaling 13604904 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034698 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 30022298 bp After Masking: 10838123 bp Masked: 63.90 % -- Input Database Coverage: 40042282 bp out of 3722616900 bp ( 1.08 % ) Sampling Time: 00:17:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:10:35 (hh:mm:ss) Elapsed Time, 45836 HSPs Collected Number of families returned by RECON: 4164 Round Time: 00:28:20 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154866 repeats masked totaling 42549796 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038781 bp Num Contigs Represented = 273 Non ambiguous bp: Initial: 90010581 bp After Masking: 31736294 bp Masked: 64.74 % -- Input Database Coverage: 130081063 bp out of 3722616900 bp ( 3.49 % ) Sampling Time: 00:40:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2614041 Comparison Time: 00:47:27 (hh:mm:ss) Elapsed Time, 280171 HSPs Collected Number of families returned by RECON: 11496 Round Time: 01:32:57 (hh:mm:ss) Elapsed Time : 544 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:41:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 522523 repeats masked totaling 142651689 bp(s). - TE Masking time 00:06:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270105276 bp Num Contigs Represented = 727 Non ambiguous bp: Initial: 270014481 bp After Masking: 79955225 bp Masked: 70.39 % -- Input Database Coverage: 400186339 bp out of 3722616900 bp ( 10.75 % ) Sampling Time: 02:07:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23574411 Comparison Time: 04:47:58 (hh:mm:ss) Elapsed Time, 798200 HSPs Collected Number of families returned by RECON: 28602 Round Time: 07:18:35 (hh:mm:ss) Elapsed Time : 1498 families discovered. RepeatScout/RECON discovery complete: 3234 families found Classification Time: 00:58:48 (hh:mm:ss) Elapsed Time Program Time: 10:48:54 (hh:mm:ss) Elapsed Time