RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VurtZ1/RM_39314.SatJan142255592023 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: 1673765758 Database = /dev/shm/rModeler.VurtZ1/GCA_009764475.1_sPriPec2.pri - Sequences = 173 - Bases = 2267857790 - N50 = 102490209 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 139971069-149968914 |* [ 3 ] 129973224-139971068 | [ ] 119975379-129973223 | [ 1 ] 109977534-119975378 | [ 2 ] 99979690-109977534 |* [ 4 ] 89981845-99979689 | [ ] 79984000-89981844 | [ 1 ] 69986155-79983999 | [ ] 59988310-69986154 | [ ] 49990466-59988310 |* [ 4 ] 39992621-49990465 |* [ 5 ] 29994776-39992620 |** [ 8 ] 19996931-29994775 |* [ 5 ] 9999086-19996930 |** [ 6 ] 1242-9999086 |************************************************** [ 134 ] Storage Throughput = excellent ( 1259.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40289641 bp ( 40011947 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:20 (hh:mm:ss) Elapsed Time Round Time: 00:19:37 (hh:mm:ss) Elapsed Time : 322 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17655 repeats masked totaling 4224250 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10160968 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10035938 bp After Masking: 5697057 bp Masked: 43.23 % -- Input Database Coverage: 10160968 bp out of 2267857790 bp ( 0.45 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:33 (hh:mm:ss) Elapsed Time, 7460 HSPs Collected Number of families returned by RECON: 871 Round Time: 00:07:22 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57103 repeats masked totaling 13825605 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30168526 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30015862 bp After Masking: 15883916 bp Masked: 47.08 % -- Input Database Coverage: 40329494 bp out of 2267857790 bp ( 1.78 % ) Sampling Time: 00:03:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:22:31 (hh:mm:ss) Elapsed Time, 22155 HSPs Collected Number of families returned by RECON: 2232 Round Time: 00:26:51 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181981 repeats masked totaling 43632158 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90977239 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90008593 bp After Masking: 45427321 bp Masked: 49.53 % -- Input Database Coverage: 131306733 bp out of 2267857790 bp ( 5.79 % ) Sampling Time: 00:10:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 02:11:33 (hh:mm:ss) Elapsed Time, 89379 HSPs Collected Number of families returned by RECON: 7591 Round Time: 02:25:15 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 589708 repeats masked totaling 140314427 bp(s). - TE Masking time 00:07:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272246472 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 270002219 bp After Masking: 126758616 bp Masked: 53.05 % -- Input Database Coverage: 403553205 bp out of 2267857790 bp ( 17.79 % ) Sampling Time: 00:34:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23266431 Comparison Time: 15:26:34 (hh:mm:ss) Elapsed Time, 208362 HSPs Collected Number of families returned by RECON: 24492 Round Time: 16:20:31 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatScout/RECON discovery complete: 1021 families found Classification Time: 00:46:34 (hh:mm:ss) Elapsed Time Program Time: 20:26:10 (hh:mm:ss) Elapsed Time