RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HI1F2y/RM_177270.MonMar112152302024 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: 1710219150 Database = /dev/shm/rModeler.HI1F2y/GCA_030848825.1_DD_mTadBra1_pri - Sequences = 148 - Bases = 2283188801 - N50 = 111368843 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 233667289-250357659 | [ 1 ] 216976919-233667288 | [ ] 200286550-216976919 | [ ] 183596180-200286549 | [ ] 166905811-183596180 | [ ] 150215441-166905810 | [ ] 133525072-150215441 | [ 1 ] 116834702-133525071 | [ 2 ] 100144333-116834702 |*** [ 8 ] 83453963-100144332 | [ 2 ] 66763594-83453963 |** [ 5 ] 50073224-66763593 | [ 2 ] 33382855-50073224 | [ 1 ] 16692485-33382854 | [ 1 ] 2116-16692485 |************************************************** [ 125 ] Storage Throughput = excellent ( 1228.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011451 bp ( 40011451 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:15 (hh:mm:ss) Elapsed Time Round Time: 00:27:35 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12407 repeats masked totaling 2638986 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000566 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000566 bp After Masking: 7251173 bp Masked: 27.49 % -- Input Database Coverage: 10000566 bp out of 2283188801 bp ( 0.44 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 5708 HSPs Collected Number of families returned by RECON: 867 Round Time: 00:07:03 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38982 repeats masked totaling 8403457 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010805 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30010805 bp After Masking: 21220804 bp Masked: 29.29 % -- Input Database Coverage: 40011371 bp out of 2283188801 bp ( 1.75 % ) Sampling Time: 00:03:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:19 (hh:mm:ss) Elapsed Time, 32253 HSPs Collected Number of families returned by RECON: 2445 Round Time: 00:33:41 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127905 repeats masked totaling 28233497 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004346 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90004106 bp After Masking: 60630529 bp Masked: 32.64 % -- Input Database Coverage: 130015717 bp out of 2283188801 bp ( 5.69 % ) Sampling Time: 00:09:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:43:56 (hh:mm:ss) Elapsed Time, 94009 HSPs Collected Number of families returned by RECON: 8876 Round Time: 02:57:16 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415108 repeats masked totaling 93658156 bp(s). - TE Masking time 00:05:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014177 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270012944 bp After Masking: 172424205 bp Masked: 36.14 % -- Input Database Coverage: 400029894 bp out of 2283188801 bp ( 17.52 % ) Sampling Time: 00:29:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 22:15:26 (hh:mm:ss) Elapsed Time, 263214 HSPs Collected Number of families returned by RECON: 36250 Round Time: 23:09:47 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatScout/RECON discovery complete: 895 families found Classification Time: 00:38:04 (hh:mm:ss) Elapsed Time Program Time: 27:53:26 (hh:mm:ss) Elapsed Time