RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ybNe7D/RM_1370414.MonMar240630412025 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: 1742823039 Database = /dev/shm/rModeler.ybNe7D/GCA_965183785.1_bPlaLeu2.hap2.1 - Sequences = 408 - Bases = 1190439839 - N50 = 127765968 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 159151339-170519221 | [ 1 ] 147783458-159151339 | [ ] 136415576-147783457 | [ ] 125047695-136415576 | [ 3 ] 113679814-125047695 | [ ] 102311932-113679813 | [ ] 90944051-102311932 | [ 1 ] 79576169-90944050 | [ 1 ] 68208288-79576169 | [ 1 ] 56840407-68208288 | [ 1 ] 45472525-56840406 | [ 1 ] 34104644-45472525 | [ ] 22736762-34104643 | [ 2 ] 11368881-22736762 | [ 5 ] 1000-11368881 |************************************************** [ 392 ] Storage Throughput = excellent ( 1855.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032108 bp ( 40026308 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:55 (hh:mm:ss) Elapsed Time Round Time: 00:10:25 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1314 repeats masked totaling 510790 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039397 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10036997 bp After Masking: 9320012 bp Masked: 7.14 % -- Input Database Coverage: 10039397 bp out of 1190439839 bp ( 0.84 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:08 (hh:mm:ss) Elapsed Time, 685 HSPs Collected Number of families returned by RECON: 287 Round Time: 00:03:45 (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 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4159 repeats masked totaling 1592299 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032557 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30029157 bp After Masking: 27400708 bp Masked: 8.75 % -- Input Database Coverage: 40071954 bp out of 1190439839 bp ( 3.37 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:15:06 (hh:mm:ss) Elapsed Time, 25474 HSPs Collected Number of families returned by RECON: 1596 Round Time: 00:18:29 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15593 repeats masked totaling 5698375 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039546 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 90032263 bp After Masking: 81527729 bp Masked: 9.45 % -- Input Database Coverage: 130111500 bp out of 1190439839 bp ( 10.93 % ) Sampling Time: 00:04:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:38:46 (hh:mm:ss) Elapsed Time, 112599 HSPs Collected Number of families returned by RECON: 8901 Round Time: 01:48:09 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62559 repeats masked totaling 23443779 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062977 bp Num Contigs Represented = 212 Non ambiguous bp: Initial: 270032358 bp After Masking: 238352206 bp Masked: 11.73 % -- Input Database Coverage: 400174477 bp out of 1190439839 bp ( 33.62 % ) Sampling Time: 00:14:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 11:51:28 (hh:mm:ss) Elapsed Time, 352587 HSPs Collected Number of families returned by RECON: 54879 Round Time: 12:29:01 (hh:mm:ss) Elapsed Time : 262 families discovered. RepeatScout/RECON discovery complete: 458 families found Classification Time: 00:16:36 (hh:mm:ss) Elapsed Time Program Time: 15:06:25 (hh:mm:ss) Elapsed Time