RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.OcnWK3/RM_1523777.TueJan211212262025 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: 1737490344 Database = /data/tmp/rModeler.OcnWK3/GCA_030012505.1_ASM3001250v1 - Sequences = 208 - Bases = 2296226205 - N50 = 165689209 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 342864635-367353949 | [ 1 ] 318375322-342864635 | [ ] 293886009-318375322 | [ ] 269396695-293886008 | [ 1 ] 244907382-269396695 | [ ] 220418069-244907382 | [ ] 195928756-220418069 | [ 1 ] 171439442-195928755 | [ ] 146950129-171439442 | [ 1 ] 122460816-146950129 | [ 3 ] 97971503-122460816 | [ 2 ] 73482189-97971502 | [ 2 ] 48992876-73482189 | [ 1 ] 24503563-48992876 |* [ 6 ] 14250-24503563 |************************************************** [ 190 ] Storage Throughput = excellent ( 1541.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005594 bp ( 40003094 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:55 (hh:mm:ss) Elapsed Time Round Time: 00:18:04 (hh:mm:ss) Elapsed Time : 579 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14348 repeats masked totaling 2948448 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024655 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10024155 bp After Masking: 6981869 bp Masked: 30.35 % -- Input Database Coverage: 10024655 bp out of 2296226205 bp ( 0.44 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:51 (hh:mm:ss) Elapsed Time, 28607 HSPs Collected Number of families returned by RECON: 1534 Round Time: 00:08:09 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46971 repeats masked totaling 9350026 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021006 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30019006 bp After Masking: 20382211 bp Masked: 32.10 % -- Input Database Coverage: 40045661 bp out of 2296226205 bp ( 1.74 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:49 (hh:mm:ss) Elapsed Time, 219226 HSPs Collected Number of families returned by RECON: 4875 Round Time: 00:33:15 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155089 repeats masked totaling 32258506 bp(s). - TE Masking time 00:01:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014520 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 90013020 bp After Masking: 57078293 bp Masked: 36.59 % -- Input Database Coverage: 130060181 bp out of 2296226205 bp ( 5.66 % ) Sampling Time: 00:07:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:29:33 (hh:mm:ss) Elapsed Time, 2073532 HSPs Collected Number of families returned by RECON: 13660 Round Time: 02:43:33 (hh:mm:ss) Elapsed Time : 427 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 529613 repeats masked totaling 110699471 bp(s). - TE Masking time 00:05:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039875 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 270032273 bp After Masking: 157036118 bp Masked: 41.85 % -- Input Database Coverage: 400100056 bp out of 2296226205 bp ( 17.42 % ) Sampling Time: 00:26:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 15:12:02 (hh:mm:ss) Elapsed Time, 32423833 HSPs Collected Number of families returned by RECON: 42035 Round Time: 16:11:01 (hh:mm:ss) Elapsed Time : 1069 families discovered. RepeatScout/RECON discovery complete: 2246 families found Classification Time: 00:41:56 (hh:mm:ss) Elapsed Time Program Time: 20:35:58 (hh:mm:ss) Elapsed Time