RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.eyUKv8/RM_3981814.SatMay131944252023 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: 1684032264 Database = /dev/shm/rModeler.eyUKv8/GCA_900880675.2_fSpaAur1.2 - 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 ( 1006.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40052708 bp ( 40038220 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:36 (hh:mm:ss) Elapsed Time Round Time: 00:21:54 (hh:mm:ss) Elapsed Time : 598 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (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... 8603 repeats masked totaling 1465670 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004276 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10002676 bp After Masking: 8352057 bp Masked: 16.50 % -- Input Database Coverage: 10004276 bp out of 833595063 bp ( 1.20 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:21 (hh:mm:ss) Elapsed Time, 10528 HSPs Collected Number of families returned by RECON: 1850 Round Time: 00:07:38 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (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... 27189 repeats masked totaling 4679377 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30048352 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30035464 bp After Masking: 24694339 bp Masked: 17.78 % -- Input Database Coverage: 40052628 bp out of 833595063 bp ( 4.80 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:32:33 (hh:mm:ss) Elapsed Time, 60503 HSPs Collected Number of families returned by RECON: 6435 Round Time: 00:37:55 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97524 repeats masked totaling 16334088 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043842 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 90005652 bp After Masking: 71543738 bp Masked: 20.51 % -- Input Database Coverage: 130096470 bp out of 833595063 bp ( 15.61 % ) Sampling Time: 00:09:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:28:19 (hh:mm:ss) Elapsed Time, 320330 HSPs Collected Number of families returned by RECON: 20521 Round Time: 03:53:22 (hh:mm:ss) Elapsed Time : 585 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 377573 repeats masked totaling 67765600 bp(s). - TE Masking time 00:12:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270105551 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 270002698 bp After Masking: 196201690 bp Masked: 27.33 % -- Input Database Coverage: 400202021 bp out of 833595063 bp ( 48.01 % ) Sampling Time: 00:33:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 25:20:54 (hh:mm:ss) Elapsed Time, 968018 HSPs Collected Number of families returned by RECON: 68196 Round Time: 27:53:03 (hh:mm:ss) Elapsed Time : 1455 families discovered. RepeatScout/RECON discovery complete: 2805 families found Classification Time: 02:18:31 (hh:mm:ss) Elapsed Time Program Time: 35:12:23 (hh:mm:ss) Elapsed Time