RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yplVXo/RM_12325.WedNov290406192023 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: 1701259578 Database = /dev/shm/rModeler.yplVXo/GCA_028451465.1_mEreDor1.pri - Sequences = 116 - Bases = 2432147792 - N50 = 132852911 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 157404616-168646601 |* [ 3 ] 146162631-157404615 | [ 1 ] 134920646-146162630 |* [ 2 ] 123678661-134920645 |** [ 5 ] 112436676-123678660 |* [ 3 ] 101194691-112436675 | [ 1 ] 89952706-101194690 | [ 1 ] 78710722-89952706 |* [ 2 ] 67468737-78710721 | [ ] 56226752-67468736 | [ ] 44984767-56226751 | [ 1 ] 33742782-44984766 | [ ] 22500797-33742781 | [ 1 ] 11258812-22500796 | [ 1 ] 16828-11258812 |************************************************** [ 95 ] Storage Throughput = excellent ( 1156.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015458 bp ( 40013260 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:37 (hh:mm:ss) Elapsed Time Round Time: 00:32:41 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13028 repeats masked totaling 2365356 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036451 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10036253 bp After Masking: 7609762 bp Masked: 24.18 % -- Input Database Coverage: 10036451 bp out of 2432147792 bp ( 0.41 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 7731 HSPs Collected Number of families returned by RECON: 946 Round Time: 00:07:31 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43706 repeats masked totaling 8154661 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018929 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30016929 bp After Masking: 21670632 bp Masked: 27.81 % -- Input Database Coverage: 40055380 bp out of 2432147792 bp ( 1.65 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:30:18 (hh:mm:ss) Elapsed Time, 22973 HSPs Collected Number of families returned by RECON: 2299 Round Time: 00:34:53 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140407 repeats masked totaling 26740514 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008452 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90007452 bp After Masking: 62621841 bp Masked: 30.43 % -- Input Database Coverage: 130063832 bp out of 2432147792 bp ( 5.35 % ) Sampling Time: 00:10:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:28:22 (hh:mm:ss) Elapsed Time, 88195 HSPs Collected Number of families returned by RECON: 8067 Round Time: 03:45:22 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 458444 repeats masked totaling 89983300 bp(s). - TE Masking time 00:06:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023915 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 270012709 bp After Masking: 178193191 bp Masked: 34.01 % -- Input Database Coverage: 400087747 bp out of 2432147792 bp ( 16.45 % ) Sampling Time: 00:33:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 27:00:35 (hh:mm:ss) Elapsed Time, 242168 HSPs Collected Number of families returned by RECON: 35152 Round Time: 28:09:22 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatScout/RECON discovery complete: 897 families found Classification Time: 00:36:05 (hh:mm:ss) Elapsed Time Program Time: 33:45:54 (hh:mm:ss) Elapsed Time