RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.iFrIel/RM_3674260.SatNov252138402023 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: 1700977119 Database = /dev/shm/rModeler.iFrIel/GCF_950005125.1_mChiNiv1.1 - Sequences = 160 - Bases = 2393390621 - N50 = 97493002 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 192171480-205897943 | [ 1 ] 178445017-192171479 | [ ] 164718554-178445016 | [ ] 150992091-164718553 | [ ] 137265628-150992090 | [ 1 ] 123539165-137265627 | [ 2 ] 109812702-123539164 | [ 2 ] 96086240-109812702 |* [ 3 ] 82359777-96086239 |* [ 3 ] 68633314-82359776 |* [ 5 ] 54906851-68633313 |** [ 6 ] 41180388-54906850 |* [ 4 ] 27453925-41180387 | [ ] 13727462-27453924 | [ ] 1000-13727462 |************************************************** [ 133 ] Storage Throughput = excellent ( 1416.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003244 bp ( 40003244 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:49 (hh:mm:ss) Elapsed Time Round Time: 00:23:48 (hh:mm:ss) Elapsed Time : 281 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15556 repeats masked totaling 2998776 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038663 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10038663 bp After Masking: 6651387 bp Masked: 33.74 % -- Input Database Coverage: 10038663 bp out of 2393390621 bp ( 0.42 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:55 (hh:mm:ss) Elapsed Time, 14473 HSPs Collected Number of families returned by RECON: 664 Round Time: 00:08:43 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48251 repeats masked totaling 9302292 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004541 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30004541 bp After Masking: 19614184 bp Masked: 34.63 % -- Input Database Coverage: 40043204 bp out of 2393390621 bp ( 1.67 % ) Sampling Time: 00:03:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:26:43 (hh:mm:ss) Elapsed Time, 28431 HSPs Collected Number of families returned by RECON: 2195 Round Time: 00:30:58 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153271 repeats masked totaling 29771737 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011271 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90010271 bp After Masking: 57146771 bp Masked: 36.51 % -- Input Database Coverage: 130054475 bp out of 2393390621 bp ( 5.43 % ) Sampling Time: 00:10:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:43:21 (hh:mm:ss) Elapsed Time, 97847 HSPs Collected Number of families returned by RECON: 8047 Round Time: 02:56:18 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 492815 repeats masked totaling 96367857 bp(s). - TE Masking time 00:06:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045243 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 270039873 bp After Masking: 165387379 bp Masked: 38.75 % -- Input Database Coverage: 400099718 bp out of 2393390621 bp ( 16.72 % ) Sampling Time: 00:32:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 21:00:33 (hh:mm:ss) Elapsed Time, 248588 HSPs Collected Number of families returned by RECON: 33825 Round Time: 21:58:09 (hh:mm:ss) Elapsed Time : 388 families discovered. RepeatScout/RECON discovery complete: 903 families found Classification Time: 00:40:57 (hh:mm:ss) Elapsed Time Program Time: 26:38:54 (hh:mm:ss) Elapsed Time