RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.vDEDjE/RM_300504.MonJan221206522024 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: 1705954011 Database = /dev/shm/rModeler.vDEDjE/GCF_950295315.1_mEriEur2.1 - Sequences = 1174 - Bases = 2720683831 - N50 = 127350028 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 196830474-210889723 | [ 2 ] 182771226-196830474 | [ 1 ] 168711978-182771226 | [ ] 154652730-168711978 | [ ] 140593482-154652730 | [ 1 ] 126534233-140593481 | [ 5 ] 112474985-126534233 | [ 2 ] 98415737-112474985 | [ 3 ] 84356489-98415737 | [ 2 ] 70297241-84356489 | [ 3 ] 56237992-70297240 | [ 2 ] 42178744-56237992 | [ 1 ] 28119496-42178744 | [ ] 14060248-28119496 | [ 2 ] 1000-14060248 |************************************************** [ 1150 ] Storage Throughput = excellent ( 1529.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016765 bp ( 40004965 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:21 (hh:mm:ss) Elapsed Time Round Time: 00:20:52 (hh:mm:ss) Elapsed Time : 260 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23893 repeats masked totaling 5088518 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012724 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10009124 bp After Masking: 4698228 bp Masked: 53.06 % -- Input Database Coverage: 10012724 bp out of 2720683831 bp ( 0.37 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:59 (hh:mm:ss) Elapsed Time, 5114 HSPs Collected Number of families returned by RECON: 365 Round Time: 00:07:11 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72168 repeats masked totaling 15482829 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30043888 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30035688 bp After Masking: 13857334 bp Masked: 53.86 % -- Input Database Coverage: 40056612 bp out of 2720683831 bp ( 1.47 % ) Sampling Time: 00:03:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:19:33 (hh:mm:ss) Elapsed Time, 10986 HSPs Collected Number of families returned by RECON: 1368 Round Time: 00:23:41 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 222034 repeats masked totaling 47794336 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042779 bp Num Contigs Represented = 131 Non ambiguous bp: Initial: 90016419 bp After Masking: 40084332 bp Masked: 55.47 % -- Input Database Coverage: 130099391 bp out of 2720683831 bp ( 4.78 % ) Sampling Time: 00:11:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 03:00:42 (hh:mm:ss) Elapsed Time, 51136 HSPs Collected Number of families returned by RECON: 5024 Round Time: 03:13:28 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 686749 repeats masked totaling 146874944 bp(s). - TE Masking time 00:04:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270089831 bp Num Contigs Represented = 300 Non ambiguous bp: Initial: 270015638 bp After Masking: 117009545 bp Masked: 56.67 % -- Input Database Coverage: 400189222 bp out of 2720683831 bp ( 14.71 % ) Sampling Time: 00:31:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 14:01:35 (hh:mm:ss) Elapsed Time, 154728 HSPs Collected Number of families returned by RECON: 19562 Round Time: 14:42:20 (hh:mm:ss) Elapsed Time : 307 families discovered. RepeatScout/RECON discovery complete: 716 families found Classification Time: 00:21:02 (hh:mm:ss) Elapsed Time Program Time: 19:08:34 (hh:mm:ss) Elapsed Time