RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.u1Nl6e/RM_6894.SunJan82301252023 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: 1673247684 Database = /dev/shm/rModeler.u1Nl6e/GCA_017976375.1_bCucCan1.pri - Sequences = 151 - Bases = 1180156273 - N50 = 122852502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195368946-209323829 | [ 1 ] 181414063-195368945 | [ ] 167459180-181414062 | [ ] 153504297-167459179 | [ 1 ] 139549415-153504297 | [ ] 125594532-139549414 | [ ] 111639649-125594531 | [ 1 ] 97684766-111639648 | [ ] 83729883-97684765 | [ ] 69775001-83729883 | [ 2 ] 55820118-69775000 | [ 1 ] 41865235-55820117 | [ 1 ] 27910352-41865234 |* [ 3 ] 13955469-27910351 |*** [ 9 ] 587-13955469 |************************************************** [ 132 ] Storage Throughput = excellent ( 1132.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40183389 bp ( 40014105 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:12 (hh:mm:ss) Elapsed Time Round Time: 00:27:31 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3389 repeats masked totaling 1043703 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028818 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10028618 bp After Masking: 8795274 bp Masked: 12.30 % -- Input Database Coverage: 10028818 bp out of 1180156273 bp ( 0.85 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:42 (hh:mm:ss) Elapsed Time, 831 HSPs Collected Number of families returned by RECON: 245 Round Time: 00:08:18 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9466 repeats masked totaling 2814308 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30194553 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30025469 bp After Masking: 26731922 bp Masked: 10.97 % -- Input Database Coverage: 40223371 bp out of 1180156273 bp ( 3.41 % ) Sampling Time: 00:03:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:33:04 (hh:mm:ss) Elapsed Time, 5742 HSPs Collected Number of families returned by RECON: 1163 Round Time: 00:37:02 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30362 repeats masked totaling 8788227 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90702112 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90038681 bp After Masking: 79474751 bp Masked: 11.73 % -- Input Database Coverage: 130925483 bp out of 1180156273 bp ( 11.09 % ) Sampling Time: 00:11:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 03:55:56 (hh:mm:ss) Elapsed Time, 52408 HSPs Collected Number of families returned by RECON: 7668 Round Time: 04:09:57 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100825 repeats masked totaling 28688864 bp(s). - TE Masking time 00:02:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271254075 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 270011057 bp After Masking: 236950857 bp Masked: 12.24 % -- Input Database Coverage: 402179558 bp out of 1180156273 bp ( 34.08 % ) Sampling Time: 00:33:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 31:19:33 (hh:mm:ss) Elapsed Time, 178622 HSPs Collected Number of families returned by RECON: 50885 Round Time: 32:20:07 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatScout/RECON discovery complete: 403 families found Classification Time: 00:27:44 (hh:mm:ss) Elapsed Time Program Time: 38:10:39 (hh:mm:ss) Elapsed Time