RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.R5JyhU/RM_468.SunJan151148092023 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: 1673812088 Database = /dev/shm/rModeler.R5JyhU/GCA_903992545.1_mPipPip1.1 - Sequences = 323 - Bases = 1763439233 - N50 = 100176833 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 190049449-203623556 | [ 2 ] 176475342-190049448 | [ 1 ] 162901235-176475341 | [ ] 149327128-162901234 | [ ] 135753021-149327127 | [ ] 122178914-135753020 | [ ] 108604807-122178913 | [ ] 95030701-108604807 | [ 2 ] 81456594-95030700 | [ 4 ] 67882487-81456593 | [ 3 ] 54308380-67882486 | [ 1 ] 40734273-54308379 | [ 5 ] 27160166-40734272 | [ 1 ] 13586059-27160165 | [ 2 ] 11953-13586059 |************************************************** [ 302 ] Storage Throughput = excellent ( 1087.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028355 bp ( 40018778 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:01 (hh:mm:ss) Elapsed Time Round Time: 00:29:34 (hh:mm:ss) Elapsed Time : 315 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13917 repeats masked totaling 2423515 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021699 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10019573 bp After Masking: 7440964 bp Masked: 25.74 % -- Input Database Coverage: 10021699 bp out of 1763439233 bp ( 0.57 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 5518 HSPs Collected Number of families returned by RECON: 884 Round Time: 00:08:14 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46485 repeats masked totaling 7825863 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046576 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30039125 bp After Masking: 21683668 bp Masked: 27.82 % -- Input Database Coverage: 40068275 bp out of 1763439233 bp ( 2.27 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:34:37 (hh:mm:ss) Elapsed Time, 23042 HSPs Collected Number of families returned by RECON: 2269 Round Time: 00:39:12 (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 : 00:05:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143066 repeats masked totaling 24626204 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038486 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90020556 bp After Masking: 63679870 bp Masked: 29.26 % -- Input Database Coverage: 130106761 bp out of 1763439233 bp ( 7.38 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:53:24 (hh:mm:ss) Elapsed Time, 121551 HSPs Collected Number of families returned by RECON: 9277 Round Time: 04:09:48 (hh:mm:ss) Elapsed Time : 222 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 474857 repeats masked totaling 82001147 bp(s). - TE Masking time 00:06:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270098562 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270022703 bp After Masking: 183259183 bp Masked: 32.13 % -- Input Database Coverage: 400205323 bp out of 1763439233 bp ( 22.69 % ) Sampling Time: 00:34:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 30:36:52 (hh:mm:ss) Elapsed Time, 258308 HSPs Collected Number of families returned by RECON: 38427 Round Time: 31:48:50 (hh:mm:ss) Elapsed Time : 426 families discovered. RepeatScout/RECON discovery complete: 1038 families found Classification Time: 00:36:18 (hh:mm:ss) Elapsed Time Program Time: 37:51:56 (hh:mm:ss) Elapsed Time