RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.iJcmoi/RM_1164146.SunDec81357062024 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: 1733695025 Database = /scratch/tmp/rModeler.iJcmoi/GCA_964263255.1_aLisVul1.1 - Sequences = 5089 - Bases = 8592455266 - N50 = 2136077662 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 2002898823-2145962954 | [ 2 ] 1859834693-2002898823 | [ ] 1716770563-1859834693 | [ 1 ] 1573706432-1716770562 | [ ] 1430642302-1573706432 | [ ] 1287578172-1430642302 | [ ] 1144514042-1287578172 | [ 1 ] 1001449911-1144514041 | [ ] 858385781-1001449911 | [ ] 715321651-858385781 | [ ] 572257521-715321651 | [ ] 429193390-572257520 | [ ] 286129260-429193390 | [ 1 ] 143065130-286129260 | [ ] 1000-143065130 |************************************************** [ 5084 ] Storage Throughput = excellent ( 1440.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025026 bp ( 40023626 non ambiguous ) - Num Contigs Represented = 107 - Sequence extraction : 00:16:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:11 (hh:mm:ss) Elapsed Time Round Time: 00:28:38 (hh:mm:ss) Elapsed Time : 722 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11790 repeats masked totaling 4437108 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030699 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10030099 bp After Masking: 4844267 bp Masked: 51.70 % -- Input Database Coverage: 10030699 bp out of 8592455266 bp ( 0.12 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:28 (hh:mm:ss) Elapsed Time, 12476 HSPs Collected Number of families returned by RECON: 1396 Round Time: 00:08:26 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:12:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33841 repeats masked totaling 13207104 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034247 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30033447 bp After Masking: 14589944 bp Masked: 51.42 % -- Input Database Coverage: 40064946 bp out of 8592455266 bp ( 0.47 % ) Sampling Time: 00:15:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:12:48 (hh:mm:ss) Elapsed Time, 77606 HSPs Collected Number of families returned by RECON: 4513 Round Time: 00:28:54 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:36:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105366 repeats masked totaling 42449465 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026795 bp Num Contigs Represented = 263 Non ambiguous bp: Initial: 90022995 bp After Masking: 40575251 bp Masked: 54.93 % -- Input Database Coverage: 130091741 bp out of 8592455266 bp ( 1.51 % ) Sampling Time: 00:44:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 00:56:38 (hh:mm:ss) Elapsed Time, 437113 HSPs Collected Number of families returned by RECON: 13148 Round Time: 01:47:11 (hh:mm:ss) Elapsed Time : 449 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:49:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 374640 repeats masked totaling 148561217 bp(s). - TE Masking time 00:04:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012417 bp Num Contigs Represented = 688 Non ambiguous bp: Initial: 270004160 bp After Masking: 100711361 bp Masked: 62.70 % -- Input Database Coverage: 400104158 bp out of 8592455266 bp ( 4.66 % ) Sampling Time: 02:10:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23239153 Comparison Time: 04:57:00 (hh:mm:ss) Elapsed Time, 1325836 HSPs Collected Number of families returned by RECON: 34914 Round Time: 07:37:48 (hh:mm:ss) Elapsed Time : 1235 families discovered. RepeatScout/RECON discovery complete: 2502 families found Classification Time: 01:01:57 (hh:mm:ss) Elapsed Time Program Time: 11:32:54 (hh:mm:ss) Elapsed Time