RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.xn02TZ/RM_176371.ThuNov140958512024 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: 1731607130 Database = /data/tmp/rModeler.xn02TZ/GCA_964211825.1_bAytFer1.hap1.1 - Sequences = 862 - Bases = 1252319576 - N50 = 85915276 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193685807-207520437 | [ 1 ] 179851178-193685807 | [ ] 166016549-179851178 | [ ] 152181920-166016549 | [ 1 ] 138347291-152181920 | [ ] 124512662-138347291 | [ ] 110678033-124512662 | [ 1 ] 96843403-110678032 | [ ] 83008774-96843403 | [ 1 ] 69174145-83008774 | [ 1 ] 55339516-69174145 | [ 1 ] 41504887-55339516 | [ 1 ] 27670258-41504887 | [ 3 ] 13835629-27670258 | [ 9 ] 1000-13835629 |************************************************** [ 843 ] Storage Throughput = good ( 822.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037735 bp ( 40035335 non ambiguous ) - Num Contigs Represented = 115 - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:43 (hh:mm:ss) Elapsed Time Round Time: 00:19:49 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2705 repeats masked totaling 1150212 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020960 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10020360 bp After Masking: 8407963 bp Masked: 16.09 % -- Input Database Coverage: 10020960 bp out of 1252319576 bp ( 0.80 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 17302 HSPs Collected Number of families returned by RECON: 330 Round Time: 00:07:12 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7006 repeats masked totaling 2722720 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016695 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 30014895 bp After Masking: 25309876 bp Masked: 15.68 % -- Input Database Coverage: 40037655 bp out of 1252319576 bp ( 3.20 % ) Sampling Time: 00:08:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:26:55 (hh:mm:ss) Elapsed Time, 6581 HSPs Collected Number of families returned by RECON: 1659 Round Time: 00:36:14 (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 : 00:03:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24557 repeats masked totaling 9402713 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013239 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 90006228 bp After Masking: 74375118 bp Masked: 17.37 % -- Input Database Coverage: 130050894 bp out of 1252319576 bp ( 10.38 % ) Sampling Time: 00:29:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 02:59:49 (hh:mm:ss) Elapsed Time, 72275 HSPs Collected Number of families returned by RECON: 9677 Round Time: 03:47:39 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:16:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75314 repeats masked totaling 28479210 bp(s). - TE Masking time 00:02:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270061995 bp Num Contigs Represented = 355 Non ambiguous bp: Initial: 270038395 bp After Masking: 222873752 bp Masked: 17.47 % -- Input Database Coverage: 400112889 bp out of 1252319576 bp ( 31.95 % ) Sampling Time: 01:28:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 22:52:10 (hh:mm:ss) Elapsed Time, 425695 HSPs Collected Number of families returned by RECON: 60268 Round Time: 24:56:47 (hh:mm:ss) Elapsed Time : 198 families discovered. RepeatScout/RECON discovery complete: 376 families found Classification Time: 00:26:18 (hh:mm:ss) Elapsed Time Program Time: 30:13:59 (hh:mm:ss) Elapsed Time