RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4O6yrG/RM_2620901.TueMar190717302024 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: 1710857850 Database = /dev/shm/rModeler.4O6yrG/GCA_036321535.1_mCamDro1.pat - Sequences = 172 - Bases = 2306619778 - N50 = 79033285 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 115066340-123284173 |* [ 3 ] 106848507-115066339 | [ 1 ] 98630675-106848507 | [ ] 90412842-98630674 |* [ 3 ] 82195010-90412842 | [ 2 ] 73977177-82195009 | [ 2 ] 65759344-73977176 |* [ 4 ] 57541512-65759344 | [ 2 ] 49323679-57541511 | [ ] 41105847-49323679 |* [ 3 ] 32888014-41105846 |* [ 5 ] 24670181-32888013 |** [ 7 ] 16452349-24670181 |* [ 5 ] 8234516-16452348 | [ 2 ] 16684-8234516 |************************************************** [ 133 ] Storage Throughput = excellent ( 1251.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031919 bp ( 40031669 non ambiguous ) - Num Contigs Represented = 85 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:42 (hh:mm:ss) Elapsed Time Round Time: 00:24:50 (hh:mm:ss) Elapsed Time : 183 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 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7030 repeats masked totaling 1597279 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003767 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10003767 bp After Masking: 6980179 bp Masked: 30.22 % -- Input Database Coverage: 10003767 bp out of 2306619778 bp ( 0.43 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 3901 HSPs Collected Number of families returned by RECON: 671 Round Time: 00:07:08 (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 : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24181 repeats masked totaling 5172021 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028072 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30027822 bp After Masking: 21813943 bp Masked: 27.35 % -- Input Database Coverage: 40031839 bp out of 2306619778 bp ( 1.74 % ) Sampling Time: 00:03:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:28:20 (hh:mm:ss) Elapsed Time, 27293 HSPs Collected Number of families returned by RECON: 2561 Round Time: 00:32:31 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84298 repeats masked totaling 19121125 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034065 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 90033265 bp After Masking: 62565838 bp Masked: 30.51 % -- Input Database Coverage: 130065904 bp out of 2306619778 bp ( 5.64 % ) Sampling Time: 00:09:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:58:12 (hh:mm:ss) Elapsed Time, 110799 HSPs Collected Number of families returned by RECON: 8974 Round Time: 03:11:18 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 279832 repeats masked totaling 63488060 bp(s). - TE Masking time 00:04:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032771 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 270027771 bp After Masking: 177815642 bp Masked: 34.15 % -- Input Database Coverage: 400098675 bp out of 2306619778 bp ( 17.35 % ) Sampling Time: 00:30:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 20:53:31 (hh:mm:ss) Elapsed Time, 702014 HSPs Collected Number of families returned by RECON: 38145 Round Time: 22:27:26 (hh:mm:ss) Elapsed Time : 337 families discovered. RepeatScout/RECON discovery complete: 768 families found Classification Time: 00:41:55 (hh:mm:ss) Elapsed Time Program Time: 27:25:08 (hh:mm:ss) Elapsed Time