RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BOzqCf/RM_27055.SunJul141829272024 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: 1721006966 Database = /dev/shm/rModeler.BOzqCf/GCF_004916995.1_NCSU_SB_2.0 - Sequences = 630 - Bases = 598127127 - N50 = 26682013 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29116852-31196601 | [ 2 ] 27037104-29116852 | [ 6 ] 24957356-27037104 | [ 5 ] 22877608-24957356 | [ 6 ] 20797860-22877608 | [ 2 ] 18718111-20797859 | [ 1 ] 16638363-18718111 | [ 1 ] 14558615-16638363 | [ ] 12478867-14558615 | [ 1 ] 10399119-12478867 | [ ] 8319370-10399118 | [ ] 6239622-8319370 | [ ] 4159874-6239622 | [ ] 2080126-4159874 | [ ] 378-2080126 |************************************************** [ 606 ] Storage Throughput = good ( 986.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40389501 bp ( 40034189 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:49 (hh:mm:ss) Elapsed Time Round Time: 00:24:01 (hh:mm:ss) Elapsed Time : 313 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (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... 6880 repeats masked totaling 493877 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10105865 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10024694 bp After Masking: 9465464 bp Masked: 5.58 % -- Input Database Coverage: 10105865 bp out of 598127127 bp ( 1.69 % ) Sampling Time: 00:00:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:06:59 (hh:mm:ss) Elapsed Time, 8678 HSPs Collected Number of families returned by RECON: 1849 Round Time: 00:07:52 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23578 repeats masked totaling 1856081 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30283556 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30009415 bp After Masking: 27954284 bp Masked: 6.85 % -- Input Database Coverage: 40389421 bp out of 598127127 bp ( 6.75 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 311655 Comparison Time: 00:40:18 (hh:mm:ss) Elapsed Time, 70956 HSPs Collected Number of families returned by RECON: 7308 Round Time: 00:44:44 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90764 repeats masked totaling 8917389 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90822088 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 90037036 bp After Masking: 80552616 bp Masked: 10.53 % -- Input Database Coverage: 131211509 bp out of 598127127 bp ( 21.94 % ) Sampling Time: 00:05:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2762425 Comparison Time: 04:43:07 (hh:mm:ss) Elapsed Time, 258589 HSPs Collected Number of families returned by RECON: 24166 Round Time: 05:07:19 (hh:mm:ss) Elapsed Time : 448 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 347080 repeats masked totaling 37235714 bp(s). - TE Masking time 00:07:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272370866 bp Num Contigs Represented = 286 Non ambiguous bp: Initial: 270034907 bp After Masking: 231093168 bp Masked: 14.42 % -- Input Database Coverage: 403582375 bp out of 598127127 bp ( 67.47 % ) Sampling Time: 00:19:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24868878 Comparison Time: 44:20:47 (hh:mm:ss) Elapsed Time, 788832 HSPs Collected Number of families returned by RECON: 91587 Round Time: 48:27:28 (hh:mm:ss) Elapsed Time : 1200 families discovered. RepeatScout/RECON discovery complete: 2156 families found Classification Time: 00:58:15 (hh:mm:ss) Elapsed Time Program Time: 55:49:39 (hh:mm:ss) Elapsed Time