RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.oSS4qB/RM_487053.WedDec41539272024 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: 1733355566 Database = /scratch/tmp/rModeler.oSS4qB/GCA_964251985.1_rPodErh1.hap2.1 - Sequences = 647 - Bases = 1477748000 - N50 = 100926544 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130837056-140182489 | [ 1 ] 121491623-130837055 | [ 2 ] 112146191-121491623 | [ ] 102800758-112146190 | [ 1 ] 93455326-102800758 | [ 3 ] 84109893-93455325 | [ 1 ] 74764460-84109892 | [ 2 ] 65419028-74764460 | [ 1 ] 56073595-65419027 | [ 2 ] 46728163-56073595 | [ 1 ] 37382730-46728162 | [ 3 ] 28037297-37382729 | [ ] 18691865-28037297 | [ ] 9346432-18691864 | [ 1 ] 1000-9346432 |************************************************** [ 629 ] Storage Throughput = excellent ( 1633.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031809 bp ( 40027609 non ambiguous ) - Num Contigs Represented = 58 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:51 (hh:mm:ss) Elapsed Time Round Time: 00:11:04 (hh:mm:ss) Elapsed Time : 533 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16400 repeats masked totaling 3081111 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019795 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10018995 bp After Masking: 6646018 bp Masked: 33.67 % -- Input Database Coverage: 10019795 bp out of 1477748000 bp ( 0.68 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:37 (hh:mm:ss) Elapsed Time, 33523 HSPs Collected Number of families returned by RECON: 1292 Round Time: 00:03:25 (hh:mm:ss) Elapsed Time : 25 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 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53574 repeats masked totaling 10098792 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011934 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30008534 bp After Masking: 19354006 bp Masked: 35.50 % -- Input Database Coverage: 40031729 bp out of 1477748000 bp ( 2.71 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:11:52 (hh:mm:ss) Elapsed Time, 45843 HSPs Collected Number of families returned by RECON: 4405 Round Time: 00:14:01 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (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... 173250 repeats masked totaling 32096219 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031612 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 90025012 bp After Masking: 56274117 bp Masked: 37.49 % -- Input Database Coverage: 130063341 bp out of 1477748000 bp ( 8.80 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 01:04:18 (hh:mm:ss) Elapsed Time, 199320 HSPs Collected Number of families returned by RECON: 14179 Round Time: 01:12:39 (hh:mm:ss) Elapsed Time : 434 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 584265 repeats masked totaling 106779438 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059310 bp Num Contigs Represented = 214 Non ambiguous bp: Initial: 270029910 bp After Masking: 157493848 bp Masked: 41.68 % -- Input Database Coverage: 400122651 bp out of 1477748000 bp ( 27.08 % ) Sampling Time: 00:13:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 07:20:33 (hh:mm:ss) Elapsed Time, 640750 HSPs Collected Number of families returned by RECON: 49280 Round Time: 08:01:18 (hh:mm:ss) Elapsed Time : 1024 families discovered. RepeatScout/RECON discovery complete: 2129 families found Classification Time: 00:31:11 (hh:mm:ss) Elapsed Time Program Time: 10:13:38 (hh:mm:ss) Elapsed Time