RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Cf5aBw/RM_2936096.FriDec80236222023 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: 1702031782 Database = /dev/shm/rModeler.Cf5aBw/GCA_963082525.1_bNesMay2.1 - Sequences = 143 - Bases = 1183271950 - N50 = 121943113 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 199875514-214152265 | [ 1 ] 185598763-199875514 | [ ] 171322012-185598763 | [ ] 157045261-171322012 | [ 1 ] 142768510-157045261 | [ ] 128491759-142768510 | [ ] 114215008-128491759 | [ 1 ] 99938257-114215008 | [ ] 85661506-99938257 | [ ] 71384755-85661506 | [ 2 ] 57108004-71384755 | [ 1 ] 42831253-57108004 | [ 1 ] 28554502-42831253 |* [ 3 ] 14277751-28554502 |*** [ 9 ] 1000-14277751 |************************************************** [ 124 ] Storage Throughput = excellent ( 1428.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043024 bp ( 40039824 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:19 (hh:mm:ss) Elapsed Time Round Time: 00:26:21 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2481 repeats masked totaling 947177 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003377 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10002577 bp After Masking: 8628928 bp Masked: 13.73 % -- Input Database Coverage: 10003377 bp out of 1183271950 bp ( 0.85 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:21 (hh:mm:ss) Elapsed Time, 1373 HSPs Collected Number of families returned by RECON: 218 Round Time: 00:09:59 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8188 repeats masked totaling 2870563 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039567 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30037167 bp After Masking: 26382103 bp Masked: 12.17 % -- Input Database Coverage: 40042944 bp out of 1183271950 bp ( 3.38 % ) Sampling Time: 00:04:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:32:29 (hh:mm:ss) Elapsed Time, 6381 HSPs Collected Number of families returned by RECON: 1314 Round Time: 00:37:49 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25988 repeats masked totaling 8819114 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034899 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90027499 bp After Masking: 79297661 bp Masked: 11.92 % -- Input Database Coverage: 130077843 bp out of 1183271950 bp ( 10.99 % ) Sampling Time: 00:11:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:52:11 (hh:mm:ss) Elapsed Time, 47557 HSPs Collected Number of families returned by RECON: 8220 Round Time: 04:05:56 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86594 repeats masked totaling 29496043 bp(s). - TE Masking time 00:03:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036825 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 270013825 bp After Masking: 233539541 bp Masked: 13.51 % -- Input Database Coverage: 400114668 bp out of 1183271950 bp ( 33.81 % ) Sampling Time: 00:41:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 28:00:03 (hh:mm:ss) Elapsed Time, 164053 HSPs Collected Number of families returned by RECON: 51576 Round Time: 29:04:14 (hh:mm:ss) Elapsed Time : 226 families discovered. RepeatScout/RECON discovery complete: 453 families found Classification Time: 00:28:38 (hh:mm:ss) Elapsed Time Program Time: 34:52:57 (hh:mm:ss) Elapsed Time