RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yMak2U/RM_22546.MonMay150746542023 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: 1684162013 Database = /dev/shm/rModeler.yMak2U/GCF_004115265.2_mRhiFer1_v1.p - Sequences = 134 - Bases = 2075768562 - N50 = 89119429 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116605865-124933378 | [ 1 ] 108278353-116605865 | [ 1 ] 99950840-108278352 |* [ 4 ] 91623328-99950840 |* [ 3 ] 83295815-91623327 |* [ 3 ] 74968303-83295815 | [ ] 66640790-74968302 |* [ 4 ] 58313278-66640790 | [ 2 ] 49985765-58313277 |* [ 4 ] 41658253-49985765 | [ 2 ] 33330740-41658252 | [ 1 ] 25003228-33330740 | [ 2 ] 16675715-25003227 | [ 2 ] 8348203-16675715 | [ 1 ] 20691-8348203 |************************************************** [ 104 ] Storage Throughput = excellent ( 1066.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40286250 bp ( 40012186 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:07 (hh:mm:ss) Elapsed Time Round Time: 00:30:06 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7974 repeats masked totaling 2159763 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10122939 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10032902 bp After Masking: 7786989 bp Masked: 22.39 % -- Input Database Coverage: 10122939 bp out of 2075768562 bp ( 0.49 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 6913 HSPs Collected Number of families returned by RECON: 1022 Round Time: 00:08:07 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25765 repeats masked totaling 6729553 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30203227 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30019200 bp After Masking: 23074503 bp Masked: 23.13 % -- Input Database Coverage: 40326166 bp out of 2075768562 bp ( 1.94 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:33:59 (hh:mm:ss) Elapsed Time, 30915 HSPs Collected Number of families returned by RECON: 2792 Round Time: 00:37:44 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89959 repeats masked totaling 22953912 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90375466 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90033900 bp After Masking: 66388427 bp Masked: 26.26 % -- Input Database Coverage: 130701632 bp out of 2075768562 bp ( 6.30 % ) Sampling Time: 00:07:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:45:33 (hh:mm:ss) Elapsed Time, 74589 HSPs Collected Number of families returned by RECON: 9379 Round Time: 03:58:41 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 308725 repeats masked totaling 77589367 bp(s). - TE Masking time 00:05:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270922771 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 270012217 bp After Masking: 190241315 bp Masked: 29.54 % -- Input Database Coverage: 401624403 bp out of 2075768562 bp ( 19.35 % ) Sampling Time: 00:25:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 28:33:30 (hh:mm:ss) Elapsed Time, 197940 HSPs Collected Number of families returned by RECON: 41174 Round Time: 29:35:37 (hh:mm:ss) Elapsed Time : 390 families discovered. RepeatScout/RECON discovery complete: 838 families found Classification Time: 00:33:17 (hh:mm:ss) Elapsed Time Program Time: 35:23:32 (hh:mm:ss) Elapsed Time