RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.O7oZMf/RM_1845387.FriJul181029062025 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: 1752859745 Database = /dev/shm/rModeler.O7oZMf/GCA_047922975.1_bEudEle1_v1.hap2 - Sequences = 359 - Bases = 965723864 - N50 = 112844502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 177535790-190216847 | [ 1 ] 164854734-177535790 | [ ] 152173677-164854733 | [ ] 139492621-152173677 | [ 1 ] 126811564-139492620 | [ ] 114130508-126811564 | [ ] 101449451-114130507 | [ 1 ] 88768395-101449451 | [ ] 76087338-88768394 | [ ] 63406282-76087338 | [ 1 ] 50725225-63406281 | [ 1 ] 38044169-50725225 | [ ] 25363112-38044168 | [ 3 ] 12682056-25363112 |* [ 9 ] 1000-12682056 |************************************************** [ 342 ] Storage Throughput = excellent ( 1096.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024410 bp ( 40023244 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:46 (hh:mm:ss) Elapsed Time Round Time: 00:35:00 (hh:mm:ss) Elapsed Time : 41 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1917 repeats masked totaling 554479 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012193 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10011927 bp After Masking: 8936460 bp Masked: 10.74 % -- Input Database Coverage: 10012193 bp out of 965723864 bp ( 1.04 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:02 (hh:mm:ss) Elapsed Time, 27738 HSPs Collected Number of families returned by RECON: 212 Round Time: 00:09:01 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4625 repeats masked totaling 1533194 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012198 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30011298 bp After Masking: 27028957 bp Masked: 9.94 % -- Input Database Coverage: 40024391 bp out of 965723864 bp ( 4.14 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:37:13 (hh:mm:ss) Elapsed Time, 4581 HSPs Collected Number of families returned by RECON: 1352 Round Time: 00:42:23 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14729 repeats masked totaling 4673816 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022840 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 90020140 bp After Masking: 80746949 bp Masked: 10.30 % -- Input Database Coverage: 130047231 bp out of 965723864 bp ( 13.47 % ) Sampling Time: 00:14:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 04:53:15 (hh:mm:ss) Elapsed Time, 56308 HSPs Collected Number of families returned by RECON: 8564 Round Time: 05:17:07 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54407 repeats masked totaling 16967185 bp(s). - TE Masking time 00:03:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034165 bp Num Contigs Represented = 194 Non ambiguous bp: Initial: 270025931 bp After Masking: 241406688 bp Masked: 10.60 % -- Input Database Coverage: 400081396 bp out of 965723864 bp ( 41.43 % ) Sampling Time: 00:43:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 40:13:27 (hh:mm:ss) Elapsed Time, 277692 HSPs Collected Number of families returned by RECON: 54399 Round Time: 42:11:26 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatScout/RECON discovery complete: 293 families found Classification Time: 00:32:36 (hh:mm:ss) Elapsed Time Program Time: 49:27:33 (hh:mm:ss) Elapsed Time