RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Gjm6jj/RM_11174.TueDec51140132023 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: 1701805212 Database = /dev/shm/rModeler.Gjm6jj/GCA_901001135.2_aRhiBiv1.2 - Sequences = 1330 - Bases = 5319239186 - N50 = 595904407 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 783702672-839681426 | [ 2 ] 727723918-783702671 | [ ] 671745164-727723917 | [ ] 615766411-671745164 | [ ] 559787657-615766410 | [ 1 ] 503808903-559787656 | [ ] 447830149-503808902 | [ 1 ] 391851396-447830149 | [ ] 335872642-391851395 | [ 2 ] 279893888-335872641 | [ 1 ] 223915134-279893887 | [ 2 ] 167936381-223915134 | [ ] 111957627-167936380 | [ 1 ] 55978873-111957626 | [ 8 ] 120-55978873 |************************************************** [ 1312 ] Storage Throughput = excellent ( 1191.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40140123 bp ( 40024070 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:10:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:17 (hh:mm:ss) Elapsed Time Round Time: 00:44:19 (hh:mm:ss) Elapsed Time : 939 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:37 (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... 17484 repeats masked totaling 5104137 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038756 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10014960 bp After Masking: 4672892 bp Masked: 53.34 % -- Input Database Coverage: 10038756 bp out of 5319239186 bp ( 0.19 % ) Sampling Time: 00:03:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:36 (hh:mm:ss) Elapsed Time, 11319 HSPs Collected Number of families returned by RECON: 1589 Round Time: 00:09:51 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53671 repeats masked totaling 15280674 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30101366 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30009109 bp After Masking: 13877171 bp Masked: 53.76 % -- Input Database Coverage: 40140122 bp out of 5319239186 bp ( 0.75 % ) Sampling Time: 00:10:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:24:56 (hh:mm:ss) Elapsed Time, 74962 HSPs Collected Number of families returned by RECON: 5365 Round Time: 00:37:48 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:22:39 (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... 176234 repeats masked totaling 50344659 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90593678 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 90020937 bp After Masking: 37410337 bp Masked: 58.44 % -- Input Database Coverage: 130733800 bp out of 5319239186 bp ( 2.46 % ) Sampling Time: 00:30:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 02:20:03 (hh:mm:ss) Elapsed Time, 352576 HSPs Collected Number of families returned by RECON: 14886 Round Time: 03:06:42 (hh:mm:ss) Elapsed Time : 515 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:07:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 600018 repeats masked totaling 171457319 bp(s). - TE Masking time 00:17:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271987427 bp Num Contigs Represented = 202 Non ambiguous bp: Initial: 270011260 bp After Masking: 91809014 bp Masked: 66.00 % -- Input Database Coverage: 402721227 bp out of 5319239186 bp ( 7.57 % ) Sampling Time: 01:36:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23334696 Comparison Time: 15:29:40 (hh:mm:ss) Elapsed Time, 809855 HSPs Collected Number of families returned by RECON: 38503 Round Time: 18:41:17 (hh:mm:ss) Elapsed Time : 1437 families discovered. RepeatScout/RECON discovery complete: 3043 families found Classification Time: 01:57:51 (hh:mm:ss) Elapsed Time Program Time: 25:17:48 (hh:mm:ss) Elapsed Time