RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.fT7bgu/RM_3854432.MonDec21730412024 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: 1733189440 Database = /scratch/tmp/rModeler.fT7bgu/GCF_949987515.2_mDelDel1.2 - Sequences = 630 - Bases = 2663516986 - N50 = 110534049 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 172543118-184867555 | [ 3 ] 160218681-172543118 | [ ] 147894244-160218681 | [ ] 135569807-147894244 | [ 2 ] 123245370-135569807 | [ 1 ] 110920933-123245370 | [ 2 ] 98596496-110920933 | [ 4 ] 86272059-98596496 | [ 4 ] 73947622-86272059 | [ 3 ] 61623185-73947622 | [ ] 49298748-61623185 | [ 2 ] 36974311-49298748 | [ ] 24649874-36974311 | [ 1 ] 12325437-24649874 | [ ] 1000-12325437 |************************************************** [ 608 ] Storage Throughput = excellent ( 1538.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024965 bp ( 40022565 non ambiguous ) - Num Contigs Represented = 125 - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:43 (hh:mm:ss) Elapsed Time Round Time: 00:16:31 (hh:mm:ss) Elapsed Time : 181 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 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8915 repeats masked totaling 2564806 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034762 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10034362 bp After Masking: 6964551 bp Masked: 30.59 % -- Input Database Coverage: 10034762 bp out of 2663516986 bp ( 0.38 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:18 (hh:mm:ss) Elapsed Time, 338721 HSPs Collected Number of families returned by RECON: 830 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30692 repeats masked totaling 10683261 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030203 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 30028203 bp After Masking: 18611359 bp Masked: 38.02 % -- Input Database Coverage: 40064965 bp out of 2663516986 bp ( 1.50 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:12:14 (hh:mm:ss) Elapsed Time, 35083 HSPs Collected Number of families returned by RECON: 2469 Round Time: 00:14:40 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104589 repeats masked totaling 33157118 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008819 bp Num Contigs Represented = 184 Non ambiguous bp: Initial: 90001588 bp After Masking: 54185617 bp Masked: 39.79 % -- Input Database Coverage: 130073784 bp out of 2663516986 bp ( 4.88 % ) Sampling Time: 00:06:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:09:54 (hh:mm:ss) Elapsed Time, 82049 HSPs Collected Number of families returned by RECON: 8016 Round Time: 01:18:37 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 353375 repeats masked totaling 109514411 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047072 bp Num Contigs Represented = 321 Non ambiguous bp: Initial: 270026412 bp After Masking: 154127549 bp Masked: 42.92 % -- Input Database Coverage: 400120856 bp out of 2663516986 bp ( 15.02 % ) Sampling Time: 00:17:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 08:14:46 (hh:mm:ss) Elapsed Time, 278597 HSPs Collected Number of families returned by RECON: 31946 Round Time: 08:48:54 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 760 families found Classification Time: 00:13:58 (hh:mm:ss) Elapsed Time Program Time: 11:00:04 (hh:mm:ss) Elapsed Time