RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.mc9IYP/RM_3473589.MonNov180542232024 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: 1731937342 Database = /scratch/tmp/rModeler.mc9IYP/GCF_036013475.1_bColLiv1.pat.W.v2 - Sequences = 869 - Bases = 1325566026 - N50 = 84824678 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198227981-212386202 | [ 1 ] 184069761-198227981 | [ ] 169911540-184069760 | [ ] 155753320-169911540 | [ 1 ] 141595099-155753319 | [ ] 127436879-141595099 | [ ] 113278658-127436878 | [ 1 ] 99120438-113278658 | [ ] 84962217-99120437 | [ ] 70803997-84962217 | [ 2 ] 56645776-70803996 | [ 1 ] 42487556-56645776 | [ ] 28329335-42487555 | [ 4 ] 14171115-28329335 | [ 9 ] 12895-14171115 |************************************************** [ 850 ] Storage Throughput = excellent ( 1601.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033239 bp ( 40031439 non ambiguous ) - Num Contigs Represented = 142 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:19 (hh:mm:ss) Elapsed Time Round Time: 00:12:28 (hh:mm:ss) Elapsed Time : 138 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2675 repeats masked totaling 971758 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013414 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10013014 bp After Masking: 8029601 bp Masked: 19.81 % -- Input Database Coverage: 10013414 bp out of 1325566026 bp ( 0.76 % ) Sampling Time: 00:08:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 7610 HSPs Collected Number of families returned by RECON: 181 Round Time: 00:11:52 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7867 repeats masked totaling 2885126 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019745 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 30018345 bp After Masking: 23743286 bp Masked: 20.90 % -- Input Database Coverage: 40033159 bp out of 1325566026 bp ( 3.02 % ) Sampling Time: 00:29:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:13:27 (hh:mm:ss) Elapsed Time, 24785 HSPs Collected Number of families returned by RECON: 1148 Round Time: 00:42:44 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:08:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23063 repeats masked totaling 7581115 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021474 bp Num Contigs Represented = 235 Non ambiguous bp: Initial: 90018774 bp After Masking: 73483906 bp Masked: 18.37 % -- Input Database Coverage: 130054633 bp out of 1325566026 bp ( 9.81 % ) Sampling Time: 01:10:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 01:25:26 (hh:mm:ss) Elapsed Time, 225736 HSPs Collected Number of families returned by RECON: 6837 Round Time: 02:39:13 (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 : 00:05:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:43:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80027 repeats masked totaling 27437289 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036832 bp Num Contigs Represented = 477 Non ambiguous bp: Initial: 270026932 bp After Masking: 214894051 bp Masked: 20.42 % -- Input Database Coverage: 400091465 bp out of 1325566026 bp ( 30.18 % ) Sampling Time: 03:50:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23416746 Comparison Time: 10:11:19 (hh:mm:ss) Elapsed Time, 1347524 HSPs Collected Number of families returned by RECON: 43332 Round Time: 14:13:13 (hh:mm:ss) Elapsed Time : 224 families discovered. RepeatScout/RECON discovery complete: 445 families found Classification Time: 00:16:19 (hh:mm:ss) Elapsed Time Program Time: 18:15:49 (hh:mm:ss) Elapsed Time