RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/901/000/725/GCF_901000725.2_fTakRub1.2/trackData/repeatModeler/RM_35148.MonDec262121132022 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: 1672118472 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/901/000/725/GCF_901000725.2_fTakRub1.2/trackData/repeatModeler/GCF_901000725.2_fTakRub1.2 - Sequences = 128 - Bases = 384126662 - N50 = 16842301 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27284512-29232231 | [ 1 ] 25336793-27284511 | [ ] 23389074-25336792 | [ ] 21441355-23389073 | [ 1 ] 19493636-21441354 | [ 2 ] 17545917-19493635 | [ 2 ] 15598198-17545916 |**** [ 9 ] 13650479-15598197 | [ 2 ] 11702760-13650478 |* [ 4 ] 9755041-11702759 | [ 1 ] 7807322-9755040 | [ ] 5859603-7807321 | [ ] 3911884-5859602 | [ ] 1964165-3911883 | [ ] 16447-1964165 |************************************************** [ 106 ] Storage Throughput = good ( 787.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40380448 bp ( 40036803 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:02 (hh:mm:ss) Elapsed Time Round Time: 00:19:36 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2735 repeats masked totaling 869742 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10049661 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10013202 bp After Masking: 8534773 bp Masked: 14.76 % -- Input Database Coverage: 10049661 bp out of 384126662 bp ( 2.62 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:30 (hh:mm:ss) Elapsed Time, 6066 HSPs Collected Number of families returned by RECON: 561 Round Time: 00:07:34 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7776 repeats masked totaling 2606264 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30330778 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30023592 bp After Masking: 26184861 bp Masked: 12.79 % -- Input Database Coverage: 40380439 bp out of 384126662 bp ( 10.51 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:28:33 (hh:mm:ss) Elapsed Time, 13995 HSPs Collected Number of families returned by RECON: 3070 Round Time: 00:33:21 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22656 repeats masked totaling 6894876 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90969648 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 90014223 bp After Masking: 79429660 bp Masked: 11.76 % -- Input Database Coverage: 131350087 bp out of 384126662 bp ( 34.19 % ) Sampling Time: 00:10:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 03:29:04 (hh:mm:ss) Elapsed Time, 118712 HSPs Collected Number of families returned by RECON: 14476 Round Time: 03:59:11 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84894 repeats masked totaling 24787027 bp(s). - TE Masking time 00:06:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 252776357 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 250386898 bp After Masking: 214461791 bp Masked: 14.35 % -- Input Database Coverage: 384126444 bp out of 384126662 bp ( 100.00 % ) Sampling Time: 00:37:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 20304378 Comparison Time: 24:07:09 (hh:mm:ss) Elapsed Time, 433561 HSPs Collected Number of families returned by RECON: 60451 Round Time: 26:52:46 (hh:mm:ss) Elapsed Time : 478 families discovered. RepeatScout/RECON discovery complete: 838 families found Classification Time: 01:38:49 (hh:mm:ss) Elapsed Time Program Time: 33:31:17 (hh:mm:ss) Elapsed Time