RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.5yDKrE/RM_253342.SatNov162029282024 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: 1731817767 Database = /scratch/tmp/rModeler.5yDKrE/GCA_037306005.1_aRhiDor1.hap1 - Sequences = 464 - Bases = 4745569335 - N50 = 571772926 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 655498946-702319255 | [ 1 ] 608678638-655498946 | [ 1 ] 561858329-608678637 | [ 2 ] 515038021-561858329 | [ ] 468217712-515038020 | [ 2 ] 421397404-468217712 | [ ] 374577095-421397403 | [ 1 ] 327756787-374577095 | [ ] 280936478-327756786 | [ ] 234116170-280936478 | [ 1 ] 187295861-234116169 | [ 2 ] 140475553-187295861 | [ ] 93655244-140475552 | [ 1 ] 46834936-93655244 | [ ] 14628-46834936 |************************************************** [ 453 ] Storage Throughput = excellent ( 1560.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032883 bp ( 40031083 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:05 (hh:mm:ss) Elapsed Time Round Time: 00:19:17 (hh:mm:ss) Elapsed Time : 806 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24119 repeats masked totaling 4910924 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000683 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10000683 bp After Masking: 4049579 bp Masked: 59.51 % -- Input Database Coverage: 10000683 bp out of 4745569335 bp ( 0.21 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:57 (hh:mm:ss) Elapsed Time, 15667 HSPs Collected Number of families returned by RECON: 1190 Round Time: 00:05:42 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77816 repeats masked totaling 16144464 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032120 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30030320 bp After Masking: 11155128 bp Masked: 62.85 % -- Input Database Coverage: 40032803 bp out of 4745569335 bp ( 0.84 % ) Sampling Time: 00:06:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:11:04 (hh:mm:ss) Elapsed Time, 40130 HSPs Collected Number of families returned by RECON: 3954 Round Time: 00:17:56 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 241376 repeats masked totaling 50379296 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042782 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90035182 bp After Masking: 30975621 bp Masked: 65.60 % -- Input Database Coverage: 130075585 bp out of 4745569335 bp ( 2.74 % ) Sampling Time: 00:19:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 00:50:31 (hh:mm:ss) Elapsed Time, 254273 HSPs Collected Number of families returned by RECON: 11480 Round Time: 01:14:38 (hh:mm:ss) Elapsed Time : 430 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:34:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 780550 repeats masked totaling 165511071 bp(s). - TE Masking time 00:04:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270029566 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 270009966 bp After Masking: 80017321 bp Masked: 70.37 % -- Input Database Coverage: 400105151 bp out of 4745569335 bp ( 8.43 % ) Sampling Time: 00:58:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 05:02:32 (hh:mm:ss) Elapsed Time, 683085 HSPs Collected Number of families returned by RECON: 31763 Round Time: 06:21:06 (hh:mm:ss) Elapsed Time : 1063 families discovered. RepeatScout/RECON discovery complete: 2424 families found Classification Time: 00:42:16 (hh:mm:ss) Elapsed Time Program Time: 09:00:55 (hh:mm:ss) Elapsed Time