RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.0Qb2g7/RM_19161.ThuDec50652142024 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: 1733410333 Database = /scratch/tmp/rModeler.0Qb2g7/GCA_036417515.1_bDroNov1.hap2 - Sequences = 238 - Bases = 1359162908 - N50 = 87007280 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206507521-221257289 | [ 1 ] 191757753-206507520 | [ ] 177007985-191757752 | [ ] 162258217-177007984 | [ 1 ] 147508449-162258216 | [ ] 132758681-147508448 | [ ] 118008913-132758680 | [ 1 ] 103259146-118008913 | [ ] 88509378-103259145 | [ ] 73759610-88509377 | [ 2 ] 59009842-73759609 | [ ] 44260074-59009841 | [ 2 ] 29510306-44260073 | [ 4 ] 14760538-29510305 |** [ 9 ] 10771-14760538 |************************************************* [ 218 ] Storage Throughput = fair ( 599.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021783 bp ( 40020783 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:58 (hh:mm:ss) Elapsed Time Round Time: 00:37:12 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1193 repeats masked totaling 601133 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010771 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10010771 bp After Masking: 8977088 bp Masked: 10.33 % -- Input Database Coverage: 10010771 bp out of 1359162908 bp ( 0.74 % ) Sampling Time: 00:01:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 1538 HSPs Collected Number of families returned by RECON: 348 Round Time: 00:07:52 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4553 repeats masked totaling 2147960 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010932 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30009932 bp After Masking: 25578137 bp Masked: 14.77 % -- Input Database Coverage: 40021703 bp out of 1359162908 bp ( 2.94 % ) Sampling Time: 00:05:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:34:14 (hh:mm:ss) Elapsed Time, 13208 HSPs Collected Number of families returned by RECON: 1741 Round Time: 00:40:34 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17225 repeats masked totaling 7131941 bp(s). - TE Masking time 00:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013771 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 90012771 bp After Masking: 76135607 bp Masked: 15.42 % -- Input Database Coverage: 130035474 bp out of 1359162908 bp ( 9.57 % ) Sampling Time: 00:19:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 04:15:15 (hh:mm:ss) Elapsed Time, 63894 HSPs Collected Number of families returned by RECON: 8394 Round Time: 05:08:47 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70151 repeats masked totaling 29436684 bp(s). - TE Masking time 00:07:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020098 bp Num Contigs Represented = 162 Non ambiguous bp: Initial: 270014332 bp After Masking: 218611900 bp Masked: 19.04 % -- Input Database Coverage: 400055572 bp out of 1359162908 bp ( 29.43 % ) Sampling Time: 01:02:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 33:20:07 (hh:mm:ss) Elapsed Time, 314577 HSPs Collected Number of families returned by RECON: 46433 Round Time: 36:14:11 (hh:mm:ss) Elapsed Time : 308 families discovered. RepeatScout/RECON discovery complete: 542 families found Classification Time: 01:18:50 (hh:mm:ss) Elapsed Time Program Time: 44:07:26 (hh:mm:ss) Elapsed Time