RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4ToJRk/RM_36910.WedJan40420312023 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: 1672834830 Database = /dev/shm/rModeler.4ToJRk/GCF_011100635.1_mTriVul1.pri - Sequences = 212 - Bases = 3359347707 - N50 = 445409394 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 530745827-568656204 | [ 1 ] 492835450-530745826 | [ ] 454925073-492835449 | [ 1 ] 417014696-454925072 | [ 2 ] 379104319-417014695 | [ ] 341193942-379104318 | [ ] 303283565-341193941 | [ 1 ] 265373189-303283565 | [ 3 ] 227462812-265373188 | [ ] 189552435-227462811 | [ 1 ] 151642058-189552434 | [ ] 113731681-151642057 | [ ] 75821304-113731680 | [ ] 37910927-75821303 | [ 1 ] 551-37910927 |************************************************** [ 202 ] Storage Throughput = good ( 990.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40122576 bp ( 40003603 non ambiguous ) - Num Contigs Represented = 16 - Sequence extraction : 00:09:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:29 (hh:mm:ss) Elapsed Time Round Time: 00:30:53 (hh:mm:ss) Elapsed Time : 389 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23761 repeats masked totaling 4267178 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080153 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10038853 bp After Masking: 5666000 bp Masked: 43.56 % -- Input Database Coverage: 10080153 bp out of 3359347707 bp ( 0.30 % ) Sampling Time: 00:02:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:59 (hh:mm:ss) Elapsed Time, 14168 HSPs Collected Number of families returned by RECON: 1197 Round Time: 00:09:16 (hh:mm:ss) Elapsed Time : 37 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:06:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77498 repeats masked totaling 14284567 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30082343 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 30004670 bp After Masking: 15323755 bp Masked: 48.93 % -- Input Database Coverage: 40162496 bp out of 3359347707 bp ( 1.20 % ) Sampling Time: 00:08:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:15 (hh:mm:ss) Elapsed Time, 30384 HSPs Collected Number of families returned by RECON: 2744 Round Time: 00:34:33 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:21:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 238976 repeats masked totaling 44230036 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90471985 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90021340 bp After Masking: 44642494 bp Masked: 50.41 % -- Input Database Coverage: 130634481 bp out of 3359347707 bp ( 3.89 % ) Sampling Time: 00:28:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:29:21 (hh:mm:ss) Elapsed Time, 110683 HSPs Collected Number of families returned by RECON: 9221 Round Time: 03:02:52 (hh:mm:ss) Elapsed Time : 217 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:55:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 762285 repeats masked totaling 140647554 bp(s). - TE Masking time 00:07:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271524804 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 270030819 bp After Masking: 125967659 bp Masked: 53.35 % -- Input Database Coverage: 402159285 bp out of 3359347707 bp ( 11.97 % ) Sampling Time: 01:14:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 17:29:42 (hh:mm:ss) Elapsed Time, 230781 HSPs Collected Number of families returned by RECON: 33408 Round Time: 19:17:14 (hh:mm:ss) Elapsed Time : 529 families discovered. RepeatScout/RECON discovery complete: 1243 families found Classification Time: 00:41:32 (hh:mm:ss) Elapsed Time Program Time: 24:16:20 (hh:mm:ss) Elapsed Time