RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jlJ6QK/RM_1299668.ThuApr101808072025 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: 1744333685 Database = /dev/shm/rModeler.jlJ6QK/GCA_049190655.1_fLepSal2.hap2 - Sequences = 1559 - Bases = 742016821 - N50 = 28436176 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 45023645-48239432 | [ 1 ] 41807858-45023644 | [ ] 38592071-41807857 | [ ] 35376284-38592070 | [ 3 ] 32160497-35376283 | [ 1 ] 28944710-32160496 | [ 4 ] 25728923-28944709 | [ 5 ] 22513137-25728923 | [ 2 ] 19297350-22513136 | [ 4 ] 16081563-19297349 | [ ] 12865776-16081562 | [ 1 ] 9649989-12865775 | [ ] 6434202-9649988 | [ ] 3218415-6434201 | [ ] 2629-3218415 |************************************************** [ 1538 ] Storage Throughput = excellent ( 1772.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026566 bp ( 40010166 non ambiguous ) - Num Contigs Represented = 225 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:27 (hh:mm:ss) Elapsed Time Round Time: 00:17:38 (hh:mm:ss) Elapsed Time : 741 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9944 repeats masked totaling 2416801 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039139 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 10035339 bp After Masking: 6234003 bp Masked: 37.88 % -- Input Database Coverage: 10039139 bp out of 742016821 bp ( 1.35 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34191 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 11380 HSPs Collected Number of families returned by RECON: 1298 Round Time: 00:04:40 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30621 repeats masked totaling 7006313 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027423 bp Num Contigs Represented = 166 Non ambiguous bp: Initial: 30014823 bp After Masking: 18890942 bp Masked: 37.06 % -- Input Database Coverage: 40066562 bp out of 742016821 bp ( 5.40 % ) Sampling Time: 00:04:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:13:38 (hh:mm:ss) Elapsed Time, 49529 HSPs Collected Number of families returned by RECON: 5168 Round Time: 00:18:18 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 99102 repeats masked totaling 21380230 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037243 bp Num Contigs Represented = 408 Non ambiguous bp: Initial: 90004343 bp After Masking: 56178185 bp Masked: 37.58 % -- Input Database Coverage: 130103805 bp out of 742016821 bp ( 17.53 % ) Sampling Time: 00:12:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2750685 Comparison Time: 01:18:13 (hh:mm:ss) Elapsed Time, 359867 HSPs Collected Number of families returned by RECON: 17656 Round Time: 01:35:42 (hh:mm:ss) Elapsed Time : 528 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 358240 repeats masked totaling 78191948 bp(s). - TE Masking time 00:07:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270137829 bp Num Contigs Represented = 875 Non ambiguous bp: Initial: 270039329 bp After Masking: 154364442 bp Masked: 42.84 % -- Input Database Coverage: 400241634 bp out of 742016821 bp ( 53.94 % ) Sampling Time: 00:43:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24798403 Comparison Time: 08:29:03 (hh:mm:ss) Elapsed Time, 1114493 HSPs Collected Number of families returned by RECON: 56439 Round Time: 09:45:54 (hh:mm:ss) Elapsed Time : 1205 families discovered. RepeatScout/RECON discovery complete: 2572 families found Classification Time: 01:04:30 (hh:mm:ss) Elapsed Time Program Time: 13:06:42 (hh:mm:ss) Elapsed Time