RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kEzBH4/RM_16033.FriJan60431122023 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: 1673008271 Database = /dev/shm/rModeler.kEzBH4/GCF_009819795.1_bAytFul2.pri - Sequences = 105 - Bases = 1127004725 - N50 = 119491689 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 193217371-207018403 | [ 1 ] 179416339-193217370 | [ ] 165615307-179416338 | [ ] 151814276-165615307 | [ 1 ] 138013244-151814275 | [ ] 124212212-138013243 | [ ] 110411180-124212211 | [ 1 ] 96610149-110411180 | [ ] 82809117-96610148 | [ 1 ] 69008085-82809116 | [ 1 ] 55207053-69008084 | [ 1 ] 41406022-55207053 | [ ] 27604990-41406021 |* [ 3 ] 13803958-27604989 |***** [ 10 ] 2927-13803958 |************************************************** [ 86 ] Storage Throughput = good ( 849.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40408001 bp ( 40010128 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:01 (hh:mm:ss) Elapsed Time Round Time: 00:27:35 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1736 repeats masked totaling 665277 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10159338 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10014165 bp After Masking: 9253888 bp Masked: 7.59 % -- Input Database Coverage: 10159338 bp out of 1127004725 bp ( 0.90 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:09:00 (hh:mm:ss) Elapsed Time, 815 HSPs Collected Number of families returned by RECON: 314 Round Time: 00:10:12 (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 : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5999 repeats masked totaling 2340749 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30288583 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30035883 bp After Masking: 27420682 bp Masked: 8.71 % -- Input Database Coverage: 40447921 bp out of 1127004725 bp ( 3.59 % ) Sampling Time: 00:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:52:55 (hh:mm:ss) Elapsed Time, 10088 HSPs Collected Number of families returned by RECON: 1914 Round Time: 00:56:38 (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 : 00:04:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18628 repeats masked totaling 6621216 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91136265 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90017495 bp After Masking: 82622176 bp Masked: 8.22 % -- Input Database Coverage: 131584186 bp out of 1127004725 bp ( 11.68 % ) Sampling Time: 00:08:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 06:52:36 (hh:mm:ss) Elapsed Time, 39750 HSPs Collected Number of families returned by RECON: 11516 Round Time: 07:07:11 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64465 repeats masked totaling 22324606 bp(s). - TE Masking time 00:03:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272316596 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 270015805 bp After Masking: 245110580 bp Masked: 9.22 % -- Input Database Coverage: 403900782 bp out of 1127004725 bp ( 35.84 % ) Sampling Time: 00:26:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23252790 Comparison Time: 57:26:14 (hh:mm:ss) Elapsed Time, 283194 HSPs Collected Number of families returned by RECON: 70989 Round Time: 59:06:37 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatScout/RECON discovery complete: 346 families found Classification Time: 00:21:44 (hh:mm:ss) Elapsed Time Program Time: 68:09:57 (hh:mm:ss) Elapsed Time