RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tRGMbM/RM_28611.SatNov252139552023 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: 1700977192 Database = /dev/shm/rModeler.tRGMbM/GCA_020745765.1_sHemOce1.mat.decon - Sequences = 4000 - Bases = 4149461884 - N50 = 58132389 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 149622794-160310095 | [ 1 ] 138935494-149622794 | [ 1 ] 128248194-138935494 | [ 1 ] 117560894-128248194 | [ 2 ] 106873594-117560894 | [ 1 ] 96186293-106873593 | [ 1 ] 85498993-96186293 | [ 4 ] 74811693-85498993 | [ 3 ] 64124393-74811693 | [ 4 ] 53437093-64124393 | [ 7 ] 42749792-53437092 | [ 8 ] 32062492-42749792 | [ 7 ] 21375192-32062492 | [ 3 ] 10687892-21375192 | [ 14 ] 592-10687892 |************************************************** [ 3943 ] Storage Throughput = excellent ( 1204.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40879012 bp ( 40013139 non ambiguous ) - Num Contigs Represented = 285 - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:58 (hh:mm:ss) Elapsed Time Round Time: 00:28:15 (hh:mm:ss) Elapsed Time : 580 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22048 repeats masked totaling 5611874 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10242159 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 10028782 bp After Masking: 3817670 bp Masked: 61.93 % -- Input Database Coverage: 10242159 bp out of 4149461884 bp ( 0.25 % ) Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:05:18 (hh:mm:ss) Elapsed Time, 4283 HSPs Collected Number of families returned by RECON: 740 Round Time: 00:08:19 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67850 repeats masked totaling 16907868 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30676867 bp Num Contigs Represented = 222 Non ambiguous bp: Initial: 30024371 bp After Masking: 11584894 bp Masked: 61.42 % -- Input Database Coverage: 40919026 bp out of 4149461884 bp ( 0.99 % ) Sampling Time: 00:07:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 304590 Comparison Time: 00:22:48 (hh:mm:ss) Elapsed Time, 25595 HSPs Collected Number of families returned by RECON: 2399 Round Time: 00:31:45 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 210837 repeats masked totaling 51175917 bp(s). - TE Masking time 00:04:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91979250 bp Num Contigs Represented = 470 Non ambiguous bp: Initial: 90035036 bp After Masking: 33195773 bp Masked: 63.13 % -- Input Database Coverage: 132898276 bp out of 4149461884 bp ( 3.20 % ) Sampling Time: 00:29:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2760075 Comparison Time: 03:59:46 (hh:mm:ss) Elapsed Time, 221329 HSPs Collected Number of families returned by RECON: 6626 Round Time: 04:34:23 (hh:mm:ss) Elapsed Time : 253 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:58:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 677253 repeats masked totaling 165369049 bp(s). - TE Masking time 00:14:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276289899 bp Num Contigs Represented = 1024 Non ambiguous bp: Initial: 270020269 bp After Masking: 87928243 bp Masked: 67.44 % -- Input Database Coverage: 409188175 bp out of 4149461884 bp ( 9.86 % ) Sampling Time: 01:23:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24798403 Comparison Time: 20:31:42 (hh:mm:ss) Elapsed Time, 1481951 HSPs Collected Number of families returned by RECON: 17852 Round Time: 22:16:21 (hh:mm:ss) Elapsed Time : 635 families discovered. RepeatScout/RECON discovery complete: 1540 families found Classification Time: 01:22:59 (hh:mm:ss) Elapsed Time Program Time: 29:22:03 (hh:mm:ss) Elapsed Time