RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.tXwedG/RM_18078.WedDec40656252024 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: 1733324184 Database = /scratch/tmp/rModeler.tXwedG/GCA_034619455.1_bLepDis1.hap1 - Sequences = 335 - Bases = 1327905210 - N50 = 83827148 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204498449-219104632 | [ 1 ] 189892266-204498449 | [ ] 175286083-189892266 | [ ] 160679900-175286083 | [ ] 146073717-160679900 | [ ] 131467534-146073717 | [ ] 116861351-131467534 | [ 1 ] 102255168-116861351 | [ ] 87648985-102255168 | [ 1 ] 73042802-87648985 | [ 3 ] 58436619-73042802 | [ 3 ] 43830436-58436619 | [ 1 ] 29224253-43830436 | [ ] 14618070-29224253 |* [ 9 ] 11887-14618070 |************************************************** [ 316 ] Storage Throughput = fair ( 638.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001708 bp ( 40000908 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:35 (hh:mm:ss) Elapsed Time Round Time: 00:28:56 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1536 repeats masked totaling 737742 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027420 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10027420 bp After Masking: 8774529 bp Masked: 12.49 % -- Input Database Coverage: 10027420 bp out of 1327905210 bp ( 0.76 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 546 HSPs Collected Number of families returned by RECON: 225 Round Time: 00:08:06 (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 : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5018 repeats masked totaling 2514702 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014208 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 30013408 bp After Masking: 26464007 bp Masked: 11.83 % -- Input Database Coverage: 40041628 bp out of 1327905210 bp ( 3.02 % ) Sampling Time: 00:04:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:34:34 (hh:mm:ss) Elapsed Time, 5219 HSPs Collected Number of families returned by RECON: 1334 Round Time: 00:39:50 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16607 repeats masked totaling 7698454 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024355 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 90020355 bp After Masking: 77728510 bp Masked: 13.65 % -- Input Database Coverage: 130065983 bp out of 1327905210 bp ( 9.79 % ) Sampling Time: 00:18:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 04:21:07 (hh:mm:ss) Elapsed Time, 64022 HSPs Collected Number of families returned by RECON: 7625 Round Time: 04:48:33 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58725 repeats masked totaling 27186024 bp(s). - TE Masking time 00:06:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044323 bp Num Contigs Represented = 189 Non ambiguous bp: Initial: 270033923 bp After Masking: 227312621 bp Masked: 15.82 % -- Input Database Coverage: 400110306 bp out of 1327905210 bp ( 30.13 % ) Sampling Time: 01:04:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 34:47:13 (hh:mm:ss) Elapsed Time, 221767 HSPs Collected Number of families returned by RECON: 48456 Round Time: 37:19:37 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatScout/RECON discovery complete: 416 families found Classification Time: 01:04:23 (hh:mm:ss) Elapsed Time Program Time: 44:29:25 (hh:mm:ss) Elapsed Time