RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KSOquy/RM_1128002.ThuJan111526362024 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: 1705015595 Database = /dev/shm/rModeler.KSOquy/GCF_027477595.1_bHaeMex1.pri - Sequences = 184 - Bases = 1148233018 - N50 = 89315722 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 148685719-159305015 | [ 1 ] 138066424-148685719 | [ ] 127447129-138066424 | [ ] 116827834-127447129 | [ 2 ] 106208539-116827834 | [ ] 95589244-106208539 | [ ] 84969949-95589244 | [ 1 ] 74350654-84969949 | [ 2 ] 63731359-74350654 | [ 1 ] 53112064-63731359 | [ ] 42492769-53112064 | [ 1 ] 31873474-42492769 | [ ] 21254179-31873474 |* [ 6 ] 10634884-21254179 |** [ 9 ] 15589-10634884 |************************************************** [ 161 ] Storage Throughput = excellent ( 1353.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40580873 bp ( 40029242 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:39 (hh:mm:ss) Elapsed Time Round Time: 00:26:21 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (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... 2447 repeats masked totaling 760104 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10147823 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10027420 bp After Masking: 8831508 bp Masked: 11.93 % -- Input Database Coverage: 10147823 bp out of 1148233018 bp ( 0.88 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:40 (hh:mm:ss) Elapsed Time, 885 HSPs Collected Number of families returned by RECON: 310 Round Time: 00:07:59 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7377 repeats masked totaling 1873945 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30433047 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30001819 bp After Masking: 26878943 bp Masked: 10.41 % -- Input Database Coverage: 40580870 bp out of 1148233018 bp ( 3.53 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:40:57 (hh:mm:ss) Elapsed Time, 8460 HSPs Collected Number of families returned by RECON: 1832 Round Time: 00:45:27 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25013 repeats masked totaling 7116096 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90733115 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90000306 bp After Masking: 78410857 bp Masked: 12.88 % -- Input Database Coverage: 131313985 bp out of 1148233018 bp ( 11.44 % ) Sampling Time: 00:11:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 03:56:52 (hh:mm:ss) Elapsed Time, 107748 HSPs Collected Number of families returned by RECON: 11679 Round Time: 04:11:38 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89019 repeats masked totaling 27190971 bp(s). - TE Masking time 00:04:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272451363 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270018976 bp After Masking: 227954272 bp Masked: 15.58 % -- Input Database Coverage: 403765348 bp out of 1148233018 bp ( 35.16 % ) Sampling Time: 00:40:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 30:56:25 (hh:mm:ss) Elapsed Time, 411076 HSPs Collected Number of families returned by RECON: 74855 Round Time: 32:54:11 (hh:mm:ss) Elapsed Time : 284 families discovered. RepeatScout/RECON discovery complete: 497 families found Classification Time: 00:54:14 (hh:mm:ss) Elapsed Time Program Time: 39:19:50 (hh:mm:ss) Elapsed Time