RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MTWu8J/RM_159933.MonJan20554302023 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: 1672667670 Database = /dev/shm/rModeler.MTWu8J/GCF_900880675.1_fSpaAur1.1 - Sequences = 176 - Bases = 833595063 - N50 = 35997798 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38634368-41392777 | [ 3 ] 35875960-38634368 |** [ 7 ] 33117552-35875960 |* [ 4 ] 30359143-33117551 |* [ 5 ] 27600735-30359143 | [ 3 ] 24842327-27600735 | [ 1 ] 22083918-24842326 | [ 1 ] 19325510-22083918 | [ ] 16567102-19325510 | [ ] 13808693-16567101 | [ ] 11050285-13808693 | [ ] 8291877-11050285 | [ ] 5533468-8291876 | [ ] 2775060-5533468 | [ ] 16652-2775060 |************************************************** [ 152 ] Storage Throughput = excellent ( 1235.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033428 bp ( 40016728 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:52 (hh:mm:ss) Elapsed Time Round Time: 00:20:44 (hh:mm:ss) Elapsed Time : 611 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8184 repeats masked totaling 1346104 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030875 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10026075 bp After Masking: 8502032 bp Masked: 15.20 % -- Input Database Coverage: 10030875 bp out of 833595063 bp ( 1.20 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:47 (hh:mm:ss) Elapsed Time, 9395 HSPs Collected Number of families returned by RECON: 1707 Round Time: 00:07:01 (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 : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27686 repeats masked totaling 4892981 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042553 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30030653 bp After Masking: 24519571 bp Masked: 18.35 % -- Input Database Coverage: 40073428 bp out of 833595063 bp ( 4.81 % ) Sampling Time: 00:02:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:29:04 (hh:mm:ss) Elapsed Time, 65385 HSPs Collected Number of families returned by RECON: 6752 Round Time: 00:34:03 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97249 repeats masked totaling 16193982 bp(s). - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043672 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90001275 bp After Masking: 71788135 bp Masked: 20.24 % -- Input Database Coverage: 130117100 bp out of 833595063 bp ( 15.61 % ) Sampling Time: 00:08:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:00:15 (hh:mm:ss) Elapsed Time, 344740 HSPs Collected Number of families returned by RECON: 20973 Round Time: 03:25:40 (hh:mm:ss) Elapsed Time : 594 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 376251 repeats masked totaling 66946630 bp(s). - TE Masking time 00:10:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270146440 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 270028866 bp After Masking: 197127513 bp Masked: 27.00 % -- Input Database Coverage: 400263540 bp out of 833595063 bp ( 48.02 % ) Sampling Time: 00:27:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 23:36:17 (hh:mm:ss) Elapsed Time, 1047763 HSPs Collected Number of families returned by RECON: 68835 Round Time: 26:27:49 (hh:mm:ss) Elapsed Time : 1405 families discovered. RepeatScout/RECON discovery complete: 2756 families found Classification Time: 02:19:51 (hh:mm:ss) Elapsed Time Program Time: 33:15:08 (hh:mm:ss) Elapsed Time