RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rHDXaq/RM_2509786.SatMar91753382024 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: 1710035618 Database = /dev/shm/rModeler.rHDXaq/GCA_022682495.1_HLdesRot8A - Sequences = 572 - Bases = 2113473284 - N50 = 167477801 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198107767-212258161 | [ 3 ] 183957374-198107767 | [ ] 169806981-183957374 | [ 1 ] 155656588-169806981 | [ 2 ] 141506195-155656588 | [ ] 127355801-141506194 | [ 2 ] 113205408-127355801 | [ 2 ] 99055015-113205408 | [ 3 ] 84904622-99055015 | [ 1 ] 70754229-84904622 | [ ] 56603835-70754228 | [ ] 42453442-56603835 | [ ] 28303049-42453442 | [ ] 14152656-28303049 | [ ] 2263-14152656 |************************************************** [ 558 ] Storage Throughput = excellent ( 1310.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038260 bp ( 40034540 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:32 (hh:mm:ss) Elapsed Time Round Time: 00:25:23 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7393 repeats masked totaling 2174058 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035399 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10034899 bp After Masking: 7771410 bp Masked: 22.56 % -- Input Database Coverage: 10035399 bp out of 2113473284 bp ( 0.47 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 71786 HSPs Collected Number of families returned by RECON: 1104 Round Time: 00:09:57 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27482 repeats masked totaling 7917130 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042781 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30039561 bp After Masking: 21658634 bp Masked: 27.90 % -- Input Database Coverage: 40078180 bp out of 2113473284 bp ( 1.90 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:27:33 (hh:mm:ss) Elapsed Time, 37359 HSPs Collected Number of families returned by RECON: 2144 Round Time: 00:32:58 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92231 repeats masked totaling 25773670 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012399 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90004602 bp After Masking: 63140169 bp Masked: 29.85 % -- Input Database Coverage: 130090579 bp out of 2113473284 bp ( 6.16 % ) Sampling Time: 00:11:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 02:52:37 (hh:mm:ss) Elapsed Time, 314863 HSPs Collected Number of families returned by RECON: 7921 Round Time: 03:06:45 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 307518 repeats masked totaling 83867501 bp(s). - TE Masking time 00:04:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039820 bp Num Contigs Represented = 200 Non ambiguous bp: Initial: 270005477 bp After Masking: 183206158 bp Masked: 32.15 % -- Input Database Coverage: 400130399 bp out of 2113473284 bp ( 18.93 % ) Sampling Time: 00:34:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 20:22:26 (hh:mm:ss) Elapsed Time, 2040888 HSPs Collected Number of families returned by RECON: 37033 Round Time: 21:20:47 (hh:mm:ss) Elapsed Time : 346 families discovered. RepeatScout/RECON discovery complete: 794 families found Classification Time: 00:29:19 (hh:mm:ss) Elapsed Time Program Time: 26:05:09 (hh:mm:ss) Elapsed Time