RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0v1fTB/RM_3349282.SunJul140726212024 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: 1720967181 Database = /dev/shm/rModeler.0v1fTB/GCF_026225935.1_ASM2622593v1 - Sequences = 600 - Bases = 941505238 - N50 = 41257348 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 44134485-47286877 | [ 4 ] 40982093-44134484 | [ 6 ] 37829701-40982092 | [ 7 ] 34677309-37829700 | [ 4 ] 31524918-34677309 | [ 1 ] 28372526-31524917 | [ ] 25220134-28372525 | [ ] 22067742-25220133 | [ 1 ] 18915350-22067741 | [ ] 15762959-18915350 | [ ] 12610567-15762958 | [ ] 9458175-12610566 | [ ] 6305783-9458174 | [ ] 3153391-6305782 | [ ] 1000-3153391 |************************************************** [ 577 ] Storage Throughput = excellent ( 1290.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40177557 bp ( 40029741 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:57 (hh:mm:ss) Elapsed Time Round Time: 00:27:22 (hh:mm:ss) Elapsed Time : 819 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 00:03:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25673 repeats masked totaling 3862913 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10048739 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10014391 bp After Masking: 5214250 bp Masked: 47.93 % -- Input Database Coverage: 10048739 bp out of 941505238 bp ( 1.07 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:07:03 (hh:mm:ss) Elapsed Time, 14365 HSPs Collected Number of families returned by RECON: 954 Round Time: 00:11:13 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76025 repeats masked totaling 11335602 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30128738 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30015270 bp After Masking: 15953796 bp Masked: 46.85 % -- Input Database Coverage: 40177477 bp out of 941505238 bp ( 4.27 % ) Sampling Time: 00:10:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:30:44 (hh:mm:ss) Elapsed Time, 34832 HSPs Collected Number of families returned by RECON: 3414 Round Time: 00:42:08 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 240273 repeats masked totaling 35742286 bp(s). - TE Masking time 00:01:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90367266 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 90006286 bp After Masking: 46339521 bp Masked: 48.52 % -- Input Database Coverage: 130544743 bp out of 941505238 bp ( 13.87 % ) Sampling Time: 00:30:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 02:49:17 (hh:mm:ss) Elapsed Time, 177430 HSPs Collected Number of families returned by RECON: 9620 Round Time: 03:25:33 (hh:mm:ss) Elapsed Time : 436 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:24:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 779003 repeats masked totaling 115386043 bp(s). - TE Masking time 00:08:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270970678 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 270006078 bp After Masking: 130173051 bp Masked: 51.79 % -- Input Database Coverage: 401515421 bp out of 941505238 bp ( 42.65 % ) Sampling Time: 01:39:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23457825 Comparison Time: 18:04:12 (hh:mm:ss) Elapsed Time, 405448 HSPs Collected Number of families returned by RECON: 32586 Round Time: 20:11:53 (hh:mm:ss) Elapsed Time : 874 families discovered. RepeatScout/RECON discovery complete: 2266 families found Classification Time: 01:06:59 (hh:mm:ss) Elapsed Time Program Time: 26:05:08 (hh:mm:ss) Elapsed Time