RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.vInzyW/RM_9556.ThuJul42001482024 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: 1720148507 Database = /dev/shm/rModeler.vInzyW/GCF_000633615.1_Guppy_female_1.0_MT - Sequences = 2767 - Bases = 731621225 - N50 = 31497199 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 43200835-46286544 | [ 1 ] 40115126-43200834 | [ ] 37029418-40115126 | [ ] 33943709-37029417 | [ 3 ] 30858001-33943709 | [ 7 ] 27772292-30858000 | [ 6 ] 24686584-27772292 | [ 4 ] 21600875-24686583 | [ 1 ] 18515167-21600875 | [ ] 15429458-18515166 | [ 1 ] 12343750-15429458 | [ ] 9258041-12343749 | [ ] 6172333-9258041 | [ ] 3086624-6172332 | [ ] 916-3086624 |************************************************** [ 2744 ] Storage Throughput = excellent ( 1090.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 44307017 bp ( 40026628 non ambiguous ) - Num Contigs Represented = 213 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:34 (hh:mm:ss) Elapsed Time Round Time: 00:24:13 (hh:mm:ss) Elapsed Time : 457 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (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... 9592 repeats masked totaling 1423694 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11029814 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 10034708 bp After Masking: 8514236 bp Masked: 15.15 % -- Input Database Coverage: 11029814 bp out of 731621225 bp ( 1.51 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 49770 Comparison Time: 00:06:49 (hh:mm:ss) Elapsed Time, 8093 HSPs Collected Number of families returned by RECON: 1506 Round Time: 00:07:58 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30812 repeats masked totaling 4705402 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 33317123 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 30031836 bp After Masking: 25053646 bp Masked: 16.58 % -- Input Database Coverage: 44346937 bp out of 731621225 bp ( 6.06 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 438516 Comparison Time: 00:39:53 (hh:mm:ss) Elapsed Time, 46839 HSPs Collected Number of families returned by RECON: 5210 Round Time: 00:43:40 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104858 repeats masked totaling 16320773 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 98685206 bp Num Contigs Represented = 405 Non ambiguous bp: Initial: 90009095 bp After Masking: 72912308 bp Masked: 18.99 % -- Input Database Coverage: 143032143 bp out of 731621225 bp ( 19.55 % ) Sampling Time: 00:06:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3851700 Comparison Time: 04:59:01 (hh:mm:ss) Elapsed Time, 225789 HSPs Collected Number of families returned by RECON: 17468 Round Time: 05:18:38 (hh:mm:ss) Elapsed Time : 414 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 392277 repeats masked totaling 63367784 bp(s). - TE Masking time 00:10:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 297628302 bp Num Contigs Represented = 1166 Non ambiguous bp: Initial: 270009167 bp After Masking: 204378580 bp Masked: 24.31 % -- Input Database Coverage: 440660445 bp out of 731621225 bp ( 60.23 % ) Sampling Time: 00:24:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35334621 Comparison Time: 38:32:24 (hh:mm:ss) Elapsed Time, 577887 HSPs Collected Number of families returned by RECON: 64328 Round Time: 40:42:47 (hh:mm:ss) Elapsed Time : 953 families discovered. RepeatScout/RECON discovery complete: 1957 families found Classification Time: 01:16:16 (hh:mm:ss) Elapsed Time Program Time: 48:33:32 (hh:mm:ss) Elapsed Time