RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ucDMhk/RM_283246.WedMar130719512024 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: 1710339588 Database = /dev/shm/rModeler.ucDMhk/GCA_035084065.1_sHydCol1.hap1 - Sequences = 1042 - Bases = 1097847766 - N50 = 91090690 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 144938675-155290691 | [ 1 ] 134586659-144938674 | [ 1 ] 124234644-134586659 | [ ] 113882628-124234643 | [ ] 103530613-113882628 | [ 1 ] 93178597-103530612 | [ ] 82826582-93178597 | [ 1 ] 72474566-82826581 | [ ] 62122551-72474566 | [ ] 51770535-62122550 | [ ] 41418520-51770535 | [ 1 ] 31066504-41418519 | [ 1 ] 20714489-31066504 | [ 4 ] 10362473-20714488 | [ 15 ] 10458-10362473 |************************************************** [ 1017 ] Storage Throughput = good ( 762.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015549 bp ( 40000149 non ambiguous ) - Num Contigs Represented = 147 - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:15 (hh:mm:ss) Elapsed Time Round Time: 00:27:18 (hh:mm:ss) Elapsed Time : 374 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26987 repeats masked totaling 4100727 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013351 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 10010551 bp After Masking: 5135061 bp Masked: 48.70 % -- Input Database Coverage: 10013351 bp out of 1097847766 bp ( 0.91 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:09 (hh:mm:ss) Elapsed Time, 10650 HSPs Collected Number of families returned by RECON: 574 Round Time: 00:09:32 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 81457 repeats masked totaling 11936103 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042125 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 30029525 bp After Masking: 15598992 bp Masked: 48.05 % -- Input Database Coverage: 40055476 bp out of 1097847766 bp ( 3.65 % ) Sampling Time: 00:12:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:24:32 (hh:mm:ss) Elapsed Time, 23425 HSPs Collected Number of families returned by RECON: 2233 Round Time: 00:37:42 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 246983 repeats masked totaling 36517314 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039242 bp Num Contigs Represented = 262 Non ambiguous bp: Initial: 90002872 bp After Masking: 46198978 bp Masked: 48.67 % -- Input Database Coverage: 130094718 bp out of 1097847766 bp ( 11.85 % ) Sampling Time: 00:39:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 02:32:31 (hh:mm:ss) Elapsed Time, 109756 HSPs Collected Number of families returned by RECON: 8339 Round Time: 03:16:09 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:28:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 810283 repeats masked totaling 119078987 bp(s). - TE Masking time 00:09:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270114074 bp Num Contigs Represented = 503 Non ambiguous bp: Initial: 270005538 bp After Masking: 130702788 bp Masked: 51.59 % -- Input Database Coverage: 400208792 bp out of 1097847766 bp ( 36.45 % ) Sampling Time: 01:47:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23622501 Comparison Time: 17:09:38 (hh:mm:ss) Elapsed Time, 369716 HSPs Collected Number of families returned by RECON: 30849 Round Time: 19:19:58 (hh:mm:ss) Elapsed Time : 533 families discovered. RepeatScout/RECON discovery complete: 1171 families found Classification Time: 00:38:55 (hh:mm:ss) Elapsed Time Program Time: 24:29:34 (hh:mm:ss) Elapsed Time