RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.c9uwug/RM_113656.SatMar231927152024 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: 1711247235 Database = /dev/shm/rModeler.c9uwug/GCA_036418225.1_bChlMac1.pat - Sequences = 343 - Bases = 1106587813 - N50 = 112928050 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 200284232-214589255 | [ 1 ] 185979209-200284231 | [ ] 171674187-185979209 | [ ] 157369164-171674186 | [ 1 ] 143064142-157369164 | [ ] 128759119-143064141 | [ ] 114454096-128759118 | [ ] 100149074-114454096 | [ 1 ] 85844051-100149073 | [ ] 71539029-85844051 | [ 2 ] 57234006-71539028 | [ ] 42928983-57234005 | [ 1 ] 28623961-42928983 | [ 2 ] 14318938-28623960 |* [ 9 ] 13916-14318938 |************************************************** [ 326 ] Storage Throughput = excellent ( 1450.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019136 bp ( 40018536 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:36 (hh:mm:ss) Elapsed Time Round Time: 00:30:30 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (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... 1744 repeats masked totaling 764228 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015853 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10015653 bp After Masking: 8848596 bp Masked: 11.65 % -- Input Database Coverage: 10015853 bp out of 1106587813 bp ( 0.91 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:56 (hh:mm:ss) Elapsed Time, 6931 HSPs Collected Number of families returned by RECON: 240 Round Time: 00:08:32 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7516 repeats masked totaling 2779041 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003205 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30002805 bp After Masking: 26222441 bp Masked: 12.60 % -- Input Database Coverage: 40019058 bp out of 1106587813 bp ( 3.62 % ) Sampling Time: 00:04:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:41:54 (hh:mm:ss) Elapsed Time, 3613 HSPs Collected Number of families returned by RECON: 1340 Round Time: 00:46:50 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19196 repeats masked totaling 7432851 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045177 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 90043577 bp After Masking: 78918237 bp Masked: 12.36 % -- Input Database Coverage: 130064235 bp out of 1106587813 bp ( 11.75 % ) Sampling Time: 00:13:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:52:09 (hh:mm:ss) Elapsed Time, 34713 HSPs Collected Number of families returned by RECON: 8419 Round Time: 04:07:05 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77932 repeats masked totaling 27261823 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042510 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 270039110 bp After Masking: 232725424 bp Masked: 13.82 % -- Input Database Coverage: 400106745 bp out of 1106587813 bp ( 36.16 % ) Sampling Time: 00:39:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 29:27:55 (hh:mm:ss) Elapsed Time, 170461 HSPs Collected Number of families returned by RECON: 52722 Round Time: 30:39:14 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatScout/RECON discovery complete: 303 families found Classification Time: 00:24:39 (hh:mm:ss) Elapsed Time Program Time: 36:36:50 (hh:mm:ss) Elapsed Time