RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CVqjZB/RM_3564853.SunFeb232339182025 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: 1740382756 Database = /dev/shm/rModeler.CVqjZB/GCA_965140245.1_bAthNoc1.hap1.1 - Sequences = 717 - Bases = 1355875761 - N50 = 88846585 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 248093529-265814424 | [ 1 ] 230372634-248093528 | [ ] 212651739-230372633 | [ ] 194930844-212651738 | [ ] 177209949-194930843 | [ ] 159489054-177209948 | [ 1 ] 141768159-159489053 | [ ] 124047264-141768158 | [ ] 106326369-124047263 | [ ] 88605474-106326368 | [ 2 ] 70884579-88605473 | [ 1 ] 53163684-70884578 | [ 2 ] 35442789-53163683 | [ 1 ] 17721894-35442788 | [ 8 ] 1000-17721894 |************************************************** [ 701 ] Storage Throughput = excellent ( 1815.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036117 bp ( 40033117 non ambiguous ) - Num Contigs Represented = 111 - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:10 (hh:mm:ss) Elapsed Time Round Time: 00:13:33 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1417 repeats masked totaling 608955 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001495 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10000295 bp After Masking: 8506238 bp Masked: 14.94 % -- Input Database Coverage: 10001495 bp out of 1355875761 bp ( 0.74 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 726 HSPs Collected Number of families returned by RECON: 287 Round Time: 00:04:12 (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 : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4602 repeats masked totaling 2138816 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034542 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 30032742 bp After Masking: 26353521 bp Masked: 12.25 % -- Input Database Coverage: 40036037 bp out of 1355875761 bp ( 2.95 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:15:18 (hh:mm:ss) Elapsed Time, 5440 HSPs Collected Number of families returned by RECON: 1551 Round Time: 00:17:19 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14840 repeats masked totaling 6151894 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012006 bp Num Contigs Represented = 191 Non ambiguous bp: Initial: 90004006 bp After Masking: 77782722 bp Masked: 13.58 % -- Input Database Coverage: 130048043 bp out of 1355875761 bp ( 9.59 % ) Sampling Time: 00:05:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:32:39 (hh:mm:ss) Elapsed Time, 56538 HSPs Collected Number of families returned by RECON: 8028 Round Time: 01:43:20 (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 : 00:07:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57779 repeats masked totaling 22442557 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028403 bp Num Contigs Represented = 392 Non ambiguous bp: Initial: 270008603 bp After Masking: 226745195 bp Masked: 16.02 % -- Input Database Coverage: 400076446 bp out of 1355875761 bp ( 29.51 % ) Sampling Time: 00:33:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23245971 Comparison Time: 11:21:27 (hh:mm:ss) Elapsed Time, 229242 HSPs Collected Number of families returned by RECON: 49177 Round Time: 12:17:28 (hh:mm:ss) Elapsed Time : 258 families discovered. RepeatScout/RECON discovery complete: 420 families found Classification Time: 00:37:15 (hh:mm:ss) Elapsed Time Program Time: 15:13:07 (hh:mm:ss) Elapsed Time