RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VfYdrr/RM_21066.TueDec191350222023 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: 1703022621 Database = /dev/shm/rModeler.VfYdrr/GCF_963514075.1_fConCon1.1 - Sequences = 380 - Bases = 1136402888 - N50 = 65176275 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 90330871-96783005 | [ 1 ] 83878737-90330870 | [ 1 ] 77426604-83878737 | [ 2 ] 70974470-77426603 | [ ] 64522336-70974469 | [ 4 ] 58070203-64522336 | [ 1 ] 51618069-58070202 | [ 2 ] 45165935-51618068 | [ 3 ] 38713802-45165935 | [ 3 ] 32261668-38713801 | [ 1 ] 25809534-32261667 | [ ] 19357401-25809534 | [ 1 ] 12905267-19357400 | [ ] 6453133-12905266 | [ ] 1000-6453133 |************************************************** [ 361 ] Storage Throughput = excellent ( 1164.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007782 bp ( 40001114 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:12 (hh:mm:ss) Elapsed Time Round Time: 00:29:37 (hh:mm:ss) Elapsed Time : 529 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10641 repeats masked totaling 1910916 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011524 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10010324 bp After Masking: 7040255 bp Masked: 29.67 % -- Input Database Coverage: 10011524 bp out of 1136402888 bp ( 0.88 % ) Sampling Time: 00:02:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 7834 HSPs Collected Number of families returned by RECON: 976 Round Time: 00:09:00 (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 : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32141 repeats masked totaling 6018031 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036252 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30030784 bp After Masking: 20696285 bp Masked: 31.08 % -- Input Database Coverage: 40047776 bp out of 1136402888 bp ( 3.52 % ) Sampling Time: 00:08:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:27:50 (hh:mm:ss) Elapsed Time, 32052 HSPs Collected Number of families returned by RECON: 3897 Round Time: 00:37:47 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 103475 repeats masked totaling 19043535 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042727 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 90025127 bp After Masking: 60724214 bp Masked: 32.55 % -- Input Database Coverage: 130090503 bp out of 1136402888 bp ( 11.45 % ) Sampling Time: 00:26:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 03:05:21 (hh:mm:ss) Elapsed Time, 205828 HSPs Collected Number of families returned by RECON: 13220 Round Time: 03:45:40 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:09:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 366540 repeats masked totaling 68347934 bp(s). - TE Masking time 00:09:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270068231 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 270025499 bp After Masking: 171497848 bp Masked: 36.49 % -- Input Database Coverage: 400158734 bp out of 1136402888 bp ( 35.21 % ) Sampling Time: 01:28:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 24:41:13 (hh:mm:ss) Elapsed Time, 797376 HSPs Collected Number of families returned by RECON: 46665 Round Time: 27:27:58 (hh:mm:ss) Elapsed Time : 1041 families discovered. RepeatScout/RECON discovery complete: 2095 families found Classification Time: 01:39:20 (hh:mm:ss) Elapsed Time Program Time: 34:09:22 (hh:mm:ss) Elapsed Time