RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Sz6g8l/RM_1640956.SunJul131736282025 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: 1752453387 Database = /dev/shm/rModeler.Sz6g8l/GCF_030445035.2_mDasNov1.1.hap2 - Sequences = 546 - Bases = 3610551914 - N50 = 130056132 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195582549-209551734 | [ 2 ] 181613364-195582548 | [ 2 ] 167644179-181613363 | [ 2 ] 153674994-167644178 | [ ] 139705810-153674994 | [ 1 ] 125736625-139705809 | [ 5 ] 111767440-125736624 | [ 2 ] 97798255-111767439 | [ 3 ] 83829070-97798254 | [ 4 ] 69859886-83829070 | [ 2 ] 55890701-69859885 | [ 3 ] 41921516-55890700 | [ 5 ] 27952331-41921515 | [ 2 ] 13983146-27952330 | [ ] 13962-13983146 |************************************************** [ 513 ] Storage Throughput = excellent ( 1235.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40159431 bp ( 40031667 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:13 (hh:mm:ss) Elapsed Time Round Time: 00:35:07 (hh:mm:ss) Elapsed Time : 334 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (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... 12920 repeats masked totaling 4270395 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027213 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10021718 bp After Masking: 5567652 bp Masked: 44.44 % -- Input Database Coverage: 10027213 bp out of 3610551914 bp ( 0.28 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:10 (hh:mm:ss) Elapsed Time, 3604 HSPs Collected Number of families returned by RECON: 668 Round Time: 00:05:56 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41410 repeats masked totaling 13372454 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30132138 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30009869 bp After Masking: 16117646 bp Masked: 46.29 % -- Input Database Coverage: 40159351 bp out of 3610551914 bp ( 1.11 % ) Sampling Time: 00:03:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:21:33 (hh:mm:ss) Elapsed Time, 31008 HSPs Collected Number of families returned by RECON: 2201 Round Time: 00:26:46 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131564 repeats masked totaling 41616197 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90268326 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 90001054 bp After Masking: 46932008 bp Masked: 47.85 % -- Input Database Coverage: 130427677 bp out of 3610551914 bp ( 3.61 % ) Sampling Time: 00:12:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 02:27:24 (hh:mm:ss) Elapsed Time, 81605 HSPs Collected Number of families returned by RECON: 6932 Round Time: 02:43:07 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 429562 repeats masked totaling 131489956 bp(s). - TE Masking time 00:09:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270953188 bp Num Contigs Represented = 150 Non ambiguous bp: Initial: 270022304 bp After Masking: 135398937 bp Masked: 49.86 % -- Input Database Coverage: 401380865 bp out of 3610551914 bp ( 11.12 % ) Sampling Time: 00:37:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 18:57:51 (hh:mm:ss) Elapsed Time, 270209 HSPs Collected Number of families returned by RECON: 26603 Round Time: 20:00:29 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatScout/RECON discovery complete: 961 families found Classification Time: 00:54:23 (hh:mm:ss) Elapsed Time Program Time: 24:45:48 (hh:mm:ss) Elapsed Time