RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.s9IFXa/RM_151816.SunJan150042172023 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: 1673772137 Database = /dev/shm/rModeler.s9IFXa/GCF_020740605.2_mLemCat1.pri - Sequences = 185 - Bases = 2245601549 - N50 = 103682405 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 267563597-286674946 | [ 1 ] 248452249-267563597 | [ ] 229340901-248452249 | [ ] 210229553-229340901 | [ ] 191118205-210229553 | [ ] 172006857-191118205 | [ ] 152895509-172006857 | [ ] 133784160-152895508 | [ 1 ] 114672812-133784160 | [ 2 ] 95561464-114672812 |** [ 7 ] 76450116-95561464 | [ 2 ] 57338768-76450116 | [ 3 ] 38227420-57338768 | [ 3 ] 19116072-38227420 |* [ 5 ] 4724-19116072 |************************************************** [ 161 ] Storage Throughput = excellent ( 1001.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40069408 bp ( 40028802 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:02:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:58 (hh:mm:ss) Elapsed Time Round Time: 00:30:41 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8578 repeats masked totaling 1823440 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039364 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10039364 bp After Masking: 7705402 bp Masked: 23.25 % -- Input Database Coverage: 10039364 bp out of 2245601549 bp ( 0.45 % ) Sampling Time: 00:02:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:02 (hh:mm:ss) Elapsed Time, 8800 HSPs Collected Number of families returned by RECON: 1163 Round Time: 00:09:11 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29182 repeats masked totaling 6160193 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30069886 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30029280 bp After Masking: 22698692 bp Masked: 24.41 % -- Input Database Coverage: 40109250 bp out of 2245601549 bp ( 1.79 % ) Sampling Time: 00:06:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:37 (hh:mm:ss) Elapsed Time, 463599 HSPs Collected Number of families returned by RECON: 2715 Round Time: 00:40:23 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97779 repeats masked totaling 21573760 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90231807 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 90031176 bp After Masking: 63806713 bp Masked: 29.13 % -- Input Database Coverage: 130341057 bp out of 2245601549 bp ( 5.80 % ) Sampling Time: 00:22:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:22:59 (hh:mm:ss) Elapsed Time, 2370402 HSPs Collected Number of families returned by RECON: 9067 Round Time: 03:50:41 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 341327 repeats masked totaling 75385817 bp(s). - TE Masking time 00:04:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270423313 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270036067 bp After Masking: 181796835 bp Masked: 32.68 % -- Input Database Coverage: 400764370 bp out of 2245601549 bp ( 17.85 % ) Sampling Time: 01:12:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 23:44:43 (hh:mm:ss) Elapsed Time, 26865857 HSPs Collected Number of families returned by RECON: 37132 Round Time: 25:42:27 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatScout/RECON discovery complete: 900 families found Classification Time: 00:44:12 (hh:mm:ss) Elapsed Time Program Time: 31:37:36 (hh:mm:ss) Elapsed Time