RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.G82qVe/RM_37634.WedDec282240182022 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: 1672296017 Database = /dev/shm/rModeler.G82qVe/GCF_901001135.1_aRhiBiv1.1 - Sequences = 1330 - Bases = 5319239201 - 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 ( 1022.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40448498 bp ( 40038703 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:11:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:34 (hh:mm:ss) Elapsed Time Round Time: 00:36:47 (hh:mm:ss) Elapsed Time : 858 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:12 (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... 17614 repeats masked totaling 4939279 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10132957 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10012644 bp After Masking: 4845309 bp Masked: 51.61 % -- Input Database Coverage: 10132957 bp out of 5319239201 bp ( 0.19 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:32 (hh:mm:ss) Elapsed Time, 13242 HSPs Collected Number of families returned by RECON: 1712 Round Time: 00:10:21 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:09:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54910 repeats masked totaling 15983264 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30315505 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30026023 bp After Masking: 13333555 bp Masked: 55.59 % -- Input Database Coverage: 40448462 bp out of 5319239201 bp ( 0.76 % ) Sampling Time: 00:12:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:22:15 (hh:mm:ss) Elapsed Time, 66551 HSPs Collected Number of families returned by RECON: 5202 Round Time: 00:36:31 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:26:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 175724 repeats masked totaling 50462537 bp(s). - TE Masking time 00:03:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90596394 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90007556 bp After Masking: 37318973 bp Masked: 58.54 % -- Input Database Coverage: 131044856 bp out of 5319239201 bp ( 2.46 % ) Sampling Time: 00:34:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 02:07:54 (hh:mm:ss) Elapsed Time, 311827 HSPs Collected Number of families returned by RECON: 14685 Round Time: 02:56:11 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:10:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 599725 repeats masked totaling 171238314 bp(s). - TE Masking time 00:13:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271657213 bp Num Contigs Represented = 221 Non ambiguous bp: Initial: 270002573 bp After Masking: 91932336 bp Masked: 65.95 % -- Input Database Coverage: 402702069 bp out of 5319239201 bp ( 7.57 % ) Sampling Time: 01:39:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23362030 Comparison Time: 13:37:48 (hh:mm:ss) Elapsed Time, 795853 HSPs Collected Number of families returned by RECON: 38328 Round Time: 16:41:26 (hh:mm:ss) Elapsed Time : 1364 families discovered. RepeatScout/RECON discovery complete: 2874 families found Classification Time: 02:01:55 (hh:mm:ss) Elapsed Time Program Time: 23:03:11 (hh:mm:ss) Elapsed Time