RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.6CxegA/RM_3209816.TueDec31034172024 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: 1733250856 Database = /scratch/tmp/rModeler.6CxegA/GCA_964289755.1_bPhaAeh10.paternal.1 - Sequences = 500 - Bases = 1165860358 - N50 = 130491745 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 209591083-224561804 | [ 1 ] 194620363-209591083 | [ ] 179649643-194620363 | [ ] 164678922-179649642 | [ 1 ] 149708202-164678922 | [ ] 134737482-149708202 | [ ] 119766762-134737482 | [ 1 ] 104796041-119766761 | [ ] 89825321-104796041 | [ ] 74854601-89825321 | [ 1 ] 59883881-74854601 | [ 1 ] 44913160-59883880 | [ ] 29942440-44913160 | [ 3 ] 14971720-29942440 | [ 8 ] 1000-14971720 |************************************************** [ 484 ] Storage Throughput = excellent ( 1519.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015758 bp ( 40006842 non ambiguous ) - Num Contigs Represented = 87 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:52 (hh:mm:ss) Elapsed Time Round Time: 00:13:51 (hh:mm:ss) Elapsed Time : 51 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 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1590 repeats masked totaling 927261 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008885 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10006769 bp After Masking: 8851128 bp Masked: 11.55 % -- Input Database Coverage: 10008885 bp out of 1165860358 bp ( 0.86 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 401 HSPs Collected Number of families returned by RECON: 214 Round Time: 00:03:43 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5138 repeats masked totaling 3155921 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006820 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30000020 bp After Masking: 26113235 bp Masked: 12.96 % -- Input Database Coverage: 40015705 bp out of 1165860358 bp ( 3.43 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:14:25 (hh:mm:ss) Elapsed Time, 3655 HSPs Collected Number of families returned by RECON: 1238 Round Time: 00:16:22 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17521 repeats masked totaling 9126861 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039014 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 90020814 bp After Masking: 78250129 bp Masked: 13.08 % -- Input Database Coverage: 130054719 bp out of 1165860358 bp ( 11.16 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:27:19 (hh:mm:ss) Elapsed Time, 31395 HSPs Collected Number of families returned by RECON: 7368 Round Time: 01:34:10 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66371 repeats masked totaling 30756698 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270079948 bp Num Contigs Represented = 282 Non ambiguous bp: Initial: 270031548 bp After Masking: 231966822 bp Masked: 14.10 % -- Input Database Coverage: 400134667 bp out of 1165860358 bp ( 34.32 % ) Sampling Time: 00:13:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23198266 Comparison Time: 10:30:28 (hh:mm:ss) Elapsed Time, 193911 HSPs Collected Number of families returned by RECON: 46598 Round Time: 10:55:27 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatScout/RECON discovery complete: 329 families found Classification Time: 00:15:55 (hh:mm:ss) Elapsed Time Program Time: 13:19:28 (hh:mm:ss) Elapsed Time