RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3yoTVe/RM_24044.TueJan31427542023 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: 1672784874 Database = /dev/shm/rModeler.3yoTVe/GCF_902459505.1_aGeoSer1.1 - Sequences = 164 - Bases = 3779430019 - N50 = 413748038 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 513817869-550518975 | [ 2 ] 477116764-513817869 | [ ] 440415658-477116763 | [ ] 403714553-440415658 | [ 1 ] 367013447-403714552 | [ ] 330312342-367013447 | [ ] 293611236-330312341 | [ 1 ] 256910131-293611236 | [ 2 ] 220209025-256910130 | [ ] 183507920-220209025 |* [ 3 ] 146806814-183507919 | [ ] 110105709-146806814 |* [ 3 ] 73404603-110105708 | [ 2 ] 36703498-73404603 |* [ 5 ] 2393-36703498 |************************************************** [ 145 ] Storage Throughput = excellent ( 1264.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40097214 bp ( 40012831 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:06:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:08 (hh:mm:ss) Elapsed Time Round Time: 00:35:07 (hh:mm:ss) Elapsed Time : 1294 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25579 repeats masked totaling 5777203 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024595 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10024295 bp After Masking: 4048396 bp Masked: 59.61 % -- Input Database Coverage: 10024595 bp out of 3779430019 bp ( 0.27 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 8164 HSPs Collected Number of families returned by RECON: 1639 Round Time: 00:08:57 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78143 repeats masked totaling 17570304 bp(s). - TE Masking time 00:01:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30112539 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30028456 bp After Masking: 11913092 bp Masked: 60.33 % -- Input Database Coverage: 40137134 bp out of 3779430019 bp ( 1.06 % ) Sampling Time: 00:07:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:22:30 (hh:mm:ss) Elapsed Time, 53405 HSPs Collected Number of families returned by RECON: 5526 Round Time: 00:32:10 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:15:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 248153 repeats masked totaling 55115842 bp(s). - TE Masking time 00:03:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90254423 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90032047 bp After Masking: 33252235 bp Masked: 63.07 % -- Input Database Coverage: 130391557 bp out of 3779430019 bp ( 3.45 % ) Sampling Time: 00:23:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:47:48 (hh:mm:ss) Elapsed Time, 298970 HSPs Collected Number of families returned by RECON: 14630 Round Time: 02:24:17 (hh:mm:ss) Elapsed Time : 634 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:47:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 820181 repeats masked totaling 182667672 bp(s). - TE Masking time 00:17:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270352894 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270003370 bp After Masking: 82658263 bp Masked: 69.39 % -- Input Database Coverage: 400744451 bp out of 3779430019 bp ( 10.60 % ) Sampling Time: 01:16:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 11:33:20 (hh:mm:ss) Elapsed Time, 885484 HSPs Collected Number of families returned by RECON: 37317 Round Time: 13:59:24 (hh:mm:ss) Elapsed Time : 1724 families discovered. RepeatScout/RECON discovery complete: 3809 families found Classification Time: 01:55:35 (hh:mm:ss) Elapsed Time Program Time: 19:35:30 (hh:mm:ss) Elapsed Time