RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Roij2x/RM_328829.ThuJan261809252023 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: 1674785364 Database = /dev/shm/rModeler.Roij2x/GCF_026419915.1_bHarHar1_primary_haplotype - Sequences = 322 - Bases = 1351447071 - N50 = 70996697 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 109248264-117051599 | [ 2 ] 101444929-109248263 | [ ] 93641594-101444928 | [ ] 85838260-93641594 | [ 2 ] 78034925-85838259 | [ 2 ] 70231590-78034924 | [ 1 ] 62428255-70231589 | [ ] 54624921-62428255 | [ 1 ] 46821586-54624920 | [ 3 ] 39018251-46821585 | [ 4 ] 31214916-39018250 | [ 3 ] 23411582-31214916 | [ 4 ] 15608247-23411581 | [ 3 ] 7804912-15608246 | [ ] 1578-7804912 |************************************************** [ 297 ] Storage Throughput = excellent ( 1312.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40079312 bp ( 40020672 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:11 (hh:mm:ss) Elapsed Time Round Time: 00:18:01 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1408 repeats masked totaling 663590 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017618 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10008524 bp After Masking: 8723698 bp Masked: 12.84 % -- Input Database Coverage: 10017618 bp out of 1351447071 bp ( 0.74 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:08 (hh:mm:ss) Elapsed Time, 655 HSPs Collected Number of families returned by RECON: 276 Round Time: 00:08:55 (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 : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4141 repeats masked totaling 1865817 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30061614 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30012068 bp After Masking: 25810988 bp Masked: 14.00 % -- Input Database Coverage: 40079232 bp out of 1351447071 bp ( 2.97 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:44:11 (hh:mm:ss) Elapsed Time, 74499 HSPs Collected Number of families returned by RECON: 1527 Round Time: 00:48:01 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15270 repeats masked totaling 6228442 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90159326 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 90013961 bp After Masking: 77591581 bp Masked: 13.80 % -- Input Database Coverage: 130238558 bp out of 1351447071 bp ( 9.64 % ) Sampling Time: 00:09:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 03:40:37 (hh:mm:ss) Elapsed Time, 379611 HSPs Collected Number of families returned by RECON: 8345 Round Time: 03:52:31 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67362 repeats masked totaling 22683210 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270442315 bp Num Contigs Represented = 166 Non ambiguous bp: Initial: 270020795 bp After Masking: 228374513 bp Masked: 15.42 % -- Input Database Coverage: 400680873 bp out of 1351447071 bp ( 29.65 % ) Sampling Time: 00:27:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 21:15:15 (hh:mm:ss) Elapsed Time, 186588 HSPs Collected Number of families returned by RECON: 51392 Round Time: 22:06:29 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatScout/RECON discovery complete: 424 families found Classification Time: 00:21:49 (hh:mm:ss) Elapsed Time Program Time: 27:35:46 (hh:mm:ss) Elapsed Time