RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7seHvl/RM_30195.SunJul211128452024 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: 1721586521 Database = /dev/shm/rModeler.7seHvl/GCF_017589495.1_AALO_Geno_1.1 - Sequences = 1095 - Bases = 854464681 - N50 = 35515461 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48565348-52034231 | [ 1 ] 45096466-48565348 | [ ] 41627584-45096466 | [ ] 38158702-41627584 | [ 1 ] 34689820-38158702 | [ 10 ] 31220938-34689820 | [ 6 ] 27752056-31220938 | [ 6 ] 24283174-27752056 | [ ] 20814292-24283174 | [ ] 17345410-20814292 | [ ] 13876528-17345410 | [ ] 10407646-13876528 | [ ] 6938764-10407646 | [ ] 3469882-6938764 | [ ] 1000-3469882 |************************************************* [ 1071 ] Storage Throughput = good ( 920.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041747 bp ( 40004747 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:58 (hh:mm:ss) Elapsed Time Round Time: 00:37:21 (hh:mm:ss) Elapsed Time : 875 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 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11116 repeats masked totaling 2483587 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10046534 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10035534 bp After Masking: 6651215 bp Masked: 33.72 % -- Input Database Coverage: 10046534 bp out of 854464681 bp ( 1.18 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:14:31 (hh:mm:ss) Elapsed Time, 5283 HSPs Collected Number of families returned by RECON: 1558 Round Time: 00:17:22 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31964 repeats masked totaling 7226408 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035163 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30009163 bp After Masking: 20310706 bp Masked: 32.32 % -- Input Database Coverage: 40081697 bp out of 854464681 bp ( 4.69 % ) Sampling Time: 00:05:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 305371 Comparison Time: 01:02:25 (hh:mm:ss) Elapsed Time, 43542 HSPs Collected Number of families returned by RECON: 5458 Round Time: 01:11:01 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102300 repeats masked totaling 22264672 bp(s). - TE Masking time 00:03:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90121367 bp Num Contigs Represented = 147 Non ambiguous bp: Initial: 90035777 bp After Masking: 60376019 bp Masked: 32.94 % -- Input Database Coverage: 130203064 bp out of 854464681 bp ( 15.24 % ) Sampling Time: 00:18:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2717946 Comparison Time: 05:40:05 (hh:mm:ss) Elapsed Time, 315845 HSPs Collected Number of families returned by RECON: 17435 Round Time: 06:19:05 (hh:mm:ss) Elapsed Time : 597 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 00:41:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 363057 repeats masked totaling 79958533 bp(s). - TE Masking time 00:17:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270253848 bp Num Contigs Represented = 345 Non ambiguous bp: Initial: 270020087 bp After Masking: 167432905 bp Masked: 37.99 % -- Input Database Coverage: 400456912 bp out of 854464681 bp ( 46.87 % ) Sampling Time: 01:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24384636 Comparison Time: 51:25:27 (hh:mm:ss) Elapsed Time, 930556 HSPs Collected Number of families returned by RECON: 60353 Round Time: 81:47:26 (hh:mm:ss) Elapsed Time : 1293 families discovered. RepeatScout/RECON discovery complete: 2848 families found Classification Time: 02:15:16 (hh:mm:ss) Elapsed Time Program Time: 92:27:31 (hh:mm:ss) Elapsed Time