RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gPWxN1/RM_2369162.WedDec60431292023 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: 1701865889 Database = /dev/shm/rModeler.gPWxN1/GCA_963383645.1_mMusAve1.1 - Sequences = 213 - Bases = 2497520702 - N50 = 131303328 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 223893691-239886027 | [ 1 ] 207901356-223893691 | [ ] 191909021-207901356 | [ 1 ] 175916686-191909021 | [ ] 159924351-175916686 | [ 2 ] 143932016-159924351 | [ ] 127939681-143932016 | [ 3 ] 111947345-127939680 |* [ 5 ] 95955010-111947345 | [ 2 ] 79962675-95955010 | [ 2 ] 63970340-79962675 | [ 2 ] 47978005-63970340 | [ 2 ] 31985670-47978005 | [ 1 ] 15993335-31985670 | [ 2 ] 1000-15993335 |************************************************** [ 190 ] Storage Throughput = good ( 997.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030980 bp ( 40022495 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:11 (hh:mm:ss) Elapsed Time Round Time: 00:23:58 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21068 repeats masked totaling 3381363 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040435 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10037235 bp After Masking: 6306228 bp Masked: 37.17 % -- Input Database Coverage: 10040435 bp out of 2497520702 bp ( 0.40 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 4855 HSPs Collected Number of families returned by RECON: 545 Round Time: 00:07:20 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65390 repeats masked totaling 10486856 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030621 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30025336 bp After Masking: 18697544 bp Masked: 37.73 % -- Input Database Coverage: 40071056 bp out of 2497520702 bp ( 1.60 % ) Sampling Time: 00:04:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:27:19 (hh:mm:ss) Elapsed Time, 19410 HSPs Collected Number of families returned by RECON: 1892 Round Time: 00:32:34 (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 : 00:06:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 203254 repeats masked totaling 32990885 bp(s). - TE Masking time 00:01:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025924 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90011724 bp After Masking: 54554775 bp Masked: 39.39 % -- Input Database Coverage: 130096980 bp out of 2497520702 bp ( 5.21 % ) Sampling Time: 00:13:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:39:34 (hh:mm:ss) Elapsed Time, 66003 HSPs Collected Number of families returned by RECON: 6062 Round Time: 03:55:06 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 635171 repeats masked totaling 105060762 bp(s). - TE Masking time 00:05:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039461 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270003239 bp After Masking: 157526777 bp Masked: 41.66 % -- Input Database Coverage: 400136441 bp out of 2497520702 bp ( 16.02 % ) Sampling Time: 00:37:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 21:11:53 (hh:mm:ss) Elapsed Time, 201247 HSPs Collected Number of families returned by RECON: 26246 Round Time: 22:32:24 (hh:mm:ss) Elapsed Time : 353 families discovered. RepeatScout/RECON discovery complete: 777 families found Classification Time: 00:29:50 (hh:mm:ss) Elapsed Time Program Time: 28:01:13 (hh:mm:ss) Elapsed Time