RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.L8p6Zz/RM_5642.MonJul151627442024 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: 1721086062 Database = /dev/shm/rModeler.L8p6Zz/GCF_008729295.1_YSFRI_Pleo_2.0 - Sequences = 94260 - Bases = 895705288 - N50 = 34146761 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38925379-41705749 | [ 2 ] 36145009-38925378 | [ 5 ] 33364639-36145008 | [ 5 ] 30584269-33364638 | [ 6 ] 27803899-30584268 | [ 2 ] 25023529-27803898 | [ 2 ] 22243159-25023528 | [ ] 19462789-22243158 | [ 1 ] 16682419-19462788 | [ ] 13902049-16682418 | [ 1 ] 11121679-13902048 | [ ] 8341309-11121678 | [ ] 5560939-8341308 | [ ] 2780569-5560938 | [ ] 200-2780569 |************************************************** [ 94236 ] Storage Throughput = excellent ( 1063.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40772504 bp ( 40022490 non ambiguous ) - Num Contigs Represented = 4474 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:38 (hh:mm:ss) Elapsed Time Round Time: 00:24:36 (hh:mm:ss) Elapsed Time : 518 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14475 repeats masked totaling 1531133 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10270372 bp Num Contigs Represented = 1148 Non ambiguous bp: Initial: 10034269 bp After Masking: 8260944 bp Masked: 17.67 % -- Input Database Coverage: 10270372 bp out of 895705288 bp ( 1.15 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 909226 Comparison Time: 00:12:55 (hh:mm:ss) Elapsed Time, 49282 HSPs Collected Number of families returned by RECON: 2164 Round Time: 00:15:10 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45735 repeats masked totaling 5296584 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30548727 bp Num Contigs Represented = 3357 Non ambiguous bp: Initial: 30034816 bp After Masking: 23912050 bp Masked: 20.39 % -- Input Database Coverage: 40819099 bp out of 895705288 bp ( 4.56 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7990003 Comparison Time: 00:56:10 (hh:mm:ss) Elapsed Time, 81024 HSPs Collected Number of families returned by RECON: 6764 Round Time: 01:02:40 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 159165 repeats masked totaling 20114602 bp(s). - TE Masking time 00:02:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91593956 bp Num Contigs Represented = 9606 Non ambiguous bp: Initial: 90005088 bp After Masking: 67382988 bp Masked: 25.13 % -- Input Database Coverage: 132413055 bp out of 895705288 bp ( 14.78 % ) Sampling Time: 00:09:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 67181436 Comparison Time: 08:07:25 (hh:mm:ss) Elapsed Time, 354073 HSPs Collected Number of families returned by RECON: 20570 Round Time: 08:40:53 (hh:mm:ss) Elapsed Time : 676 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 581107 repeats masked totaling 77852001 bp(s). - TE Masking time 00:14:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274827164 bp Num Contigs Represented = 28856 Non ambiguous bp: Initial: 270008017 bp After Masking: 184720014 bp Masked: 31.59 % -- Input Database Coverage: 407240219 bp out of 895705288 bp ( 45.47 % ) Sampling Time: 00:36:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 608010756 Comparison Time: 71:36:26 (hh:mm:ss) Elapsed Time, 753046 HSPs Collected Number of families returned by RECON: 67561 Round Time: 74:39:39 (hh:mm:ss) Elapsed Time : 1298 families discovered. RepeatScout/RECON discovery complete: 2731 families found Classification Time: 01:33:17 (hh:mm:ss) Elapsed Time Program Time: 86:36:15 (hh:mm:ss) Elapsed Time