RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.OquvN4/RM_29092.WedJul101603072024 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: 1720652586 Database = /dev/shm/rModeler.OquvN4/GCF_001970005.1_Flounder_ref_guided_V1.0 - Sequences = 9525 - Bases = 643911827 - N50 = 10900285 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 22052130-23627241 | [ 3 ] 20477019-22052129 | [ ] 18901909-20477019 | [ 1 ] 17326798-18901908 | [ 1 ] 15751687-17326797 | [ 2 ] 14176577-15751687 | [ 3 ] 12601466-14176576 | [ 7 ] 11026355-12601465 | [ 2 ] 9451245-11026355 | [ 4 ] 7876134-9451244 | [ 3 ] 6301023-7876133 | [ 5 ] 4725913-6301023 | [ 3 ] 3150802-4725912 | [ 8 ] 1575691-3150801 | [ 9 ] 581-1575691 |************************************************** [ 9474 ] Storage Throughput = excellent ( 1103.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 48824592 bp ( 40025518 non ambiguous ) - Num Contigs Represented = 855 - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:49 (hh:mm:ss) Elapsed Time Round Time: 00:23:58 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6313 repeats masked totaling 549807 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 12214480 bp Num Contigs Represented = 230 Non ambiguous bp: Initial: 10020692 bp After Masking: 9359103 bp Masked: 6.60 % -- Input Database Coverage: 12214480 bp out of 643911827 bp ( 1.90 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 93096 Comparison Time: 00:09:02 (hh:mm:ss) Elapsed Time, 7038 HSPs Collected Number of families returned by RECON: 1423 Round Time: 00:09:54 (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 : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20329 repeats masked totaling 1884589 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 36610082 bp Num Contigs Represented = 691 Non ambiguous bp: Initial: 30004826 bp After Masking: 27805898 bp Masked: 7.33 % -- Input Database Coverage: 48824562 bp out of 643911827 bp ( 7.58 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 921403 Comparison Time: 00:47:17 (hh:mm:ss) Elapsed Time, 43433 HSPs Collected Number of families returned by RECON: 5629 Round Time: 00:50:19 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73792 repeats masked totaling 7870282 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 112338050 bp Num Contigs Represented = 1941 Non ambiguous bp: Initial: 90013801 bp After Masking: 81161302 bp Masked: 9.83 % -- Input Database Coverage: 161162612 bp out of 643911827 bp ( 25.03 % ) Sampling Time: 00:04:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 8792721 Comparison Time: 05:31:40 (hh:mm:ss) Elapsed Time, 205874 HSPs Collected Number of families returned by RECON: 22335 Round Time: 05:51:16 (hh:mm:ss) Elapsed Time : 331 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 272484 repeats masked totaling 31806202 bp(s). - TE Masking time 00:05:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 331782051 bp Num Contigs Represented = 5067 Non ambiguous bp: Initial: 270007483 bp After Masking: 235332628 bp Masked: 12.84 % -- Input Database Coverage: 492944663 bp out of 643911827 bp ( 76.55 % ) Sampling Time: 00:16:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 74706976 Comparison Time: 42:41:47 (hh:mm:ss) Elapsed Time, 703013 HSPs Collected Number of families returned by RECON: 92178 Round Time: 46:03:53 (hh:mm:ss) Elapsed Time : 870 families discovered. RepeatScout/RECON discovery complete: 1555 families found Classification Time: 00:47:44 (hh:mm:ss) Elapsed Time Program Time: 54:07:04 (hh:mm:ss) Elapsed Time