RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5aVpXF/RM_11954.MonJul10525162024 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: 1719836716 Database = /dev/shm/rModeler.5aVpXF/GCA_023349555.1_fCebVio1.0.p - Sequences = 725 - Bases = 575660146 - N50 = 16527700 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 23654408-25343235 | [ 2 ] 21965581-23654407 | [ 1 ] 20276754-21965580 | [ ] 18587927-20276753 | [ 3 ] 16899100-18587926 | [ 6 ] 15210273-16899099 | [ 4 ] 13521446-15210272 | [ 1 ] 11832620-13521446 | [ 3 ] 10143793-11832619 | [ 2 ] 8454966-10143792 | [ 1 ] 6766139-8454965 | [ 2 ] 5077312-6766138 | [ 2 ] 3388485-5077311 | [ 1 ] 1699658-3388484 |* [ 23 ] 10832-1699658 |************************************************** [ 674 ] Storage Throughput = excellent ( 1053.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021094 bp ( 40014894 non ambiguous ) - Num Contigs Represented = 205 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:43 (hh:mm:ss) Elapsed Time Round Time: 00:25:48 (hh:mm:ss) Elapsed Time : 365 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6230 repeats masked totaling 925122 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040775 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 10039475 bp After Masking: 8397919 bp Masked: 16.35 % -- Input Database Coverage: 10040775 bp out of 575660146 bp ( 1.74 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:36 (hh:mm:ss) Elapsed Time, 8511 HSPs Collected Number of families returned by RECON: 1463 Round Time: 00:07:36 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19806 repeats masked totaling 2794206 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020227 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 30015327 bp After Masking: 24950256 bp Masked: 16.87 % -- Input Database Coverage: 40061002 bp out of 575660146 bp ( 6.96 % ) Sampling Time: 00:04:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 299925 Comparison Time: 00:32:18 (hh:mm:ss) Elapsed Time, 44722 HSPs Collected Number of families returned by RECON: 5149 Round Time: 00:38:35 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69273 repeats masked totaling 10279753 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016730 bp Num Contigs Represented = 276 Non ambiguous bp: Initial: 90002058 bp After Masking: 73526310 bp Masked: 18.31 % -- Input Database Coverage: 130077732 bp out of 575660146 bp ( 22.60 % ) Sampling Time: 00:11:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 03:56:23 (hh:mm:ss) Elapsed Time, 244574 HSPs Collected Number of families returned by RECON: 18720 Round Time: 04:23:36 (hh:mm:ss) Elapsed Time : 422 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 270909 repeats masked totaling 41862435 bp(s). - TE Masking time 00:08:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270077104 bp Num Contigs Represented = 499 Non ambiguous bp: Initial: 270031262 bp After Masking: 209553374 bp Masked: 22.40 % -- Input Database Coverage: 400154836 bp out of 575660146 bp ( 69.51 % ) Sampling Time: 00:41:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23801550 Comparison Time: 35:54:54 (hh:mm:ss) Elapsed Time, 752829 HSPs Collected Number of families returned by RECON: 68732 Round Time: 38:44:34 (hh:mm:ss) Elapsed Time : 1093 families discovered. RepeatScout/RECON discovery complete: 1994 families found Classification Time: 01:35:37 (hh:mm:ss) Elapsed Time Program Time: 45:55:46 (hh:mm:ss) Elapsed Time