RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nMbvYe/RM_3724408.MonMay150748192023 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: 1684162098 Database = /dev/shm/rModeler.nMbvYe/GCF_011100555.1_mCalJa1.2.pat.X - Sequences = 1233 - Bases = 2874864526 - N50 = 146897247 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202510801-216975769 | [ 2 ] 188045833-202510800 | [ 1 ] 173580866-188045833 | [ ] 159115898-173580865 | [ 3 ] 144650930-159115897 | [ 2 ] 130185963-144650930 | [ 2 ] 115720995-130185962 | [ 4 ] 101256027-115720994 | [ 1 ] 86791060-101256027 | [ 2 ] 72326092-86791059 | [ 1 ] 57861124-72326091 | [ ] 43396157-57861124 | [ 5 ] 28931189-43396156 | [ ] 14466221-28931188 | [ ] 1254-14466221 |************************************************** [ 1210 ] Storage Throughput = excellent ( 1359.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40162359 bp ( 40004438 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:02:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:14 (hh:mm:ss) Elapsed Time Round Time: 00:25:38 (hh:mm:ss) Elapsed Time : 243 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (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... 15372 repeats masked totaling 3122821 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10046590 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10021808 bp After Masking: 6736874 bp Masked: 32.78 % -- Input Database Coverage: 10046590 bp out of 2874864526 bp ( 0.35 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:51 (hh:mm:ss) Elapsed Time, 6367 HSPs Collected Number of families returned by RECON: 929 Round Time: 00:08:39 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46579 repeats masked totaling 9906501 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30155692 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30022553 bp After Masking: 19331391 bp Masked: 35.61 % -- Input Database Coverage: 40202282 bp out of 2874864526 bp ( 1.40 % ) Sampling Time: 00:04:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:33:00 (hh:mm:ss) Elapsed Time, 86904 HSPs Collected Number of families returned by RECON: 2444 Round Time: 00:38:50 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149853 repeats masked totaling 32535338 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90577971 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 90002397 bp After Masking: 55556890 bp Masked: 38.27 % -- Input Database Coverage: 130780253 bp out of 2874864526 bp ( 4.55 % ) Sampling Time: 00:13:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 03:05:44 (hh:mm:ss) Elapsed Time, 201871 HSPs Collected Number of families returned by RECON: 8131 Round Time: 03:22:25 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 479937 repeats masked totaling 104246325 bp(s). - TE Masking time 00:05:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271179575 bp Num Contigs Represented = 231 Non ambiguous bp: Initial: 270006754 bp After Masking: 159159901 bp Masked: 41.05 % -- Input Database Coverage: 401959828 bp out of 2874864526 bp ( 13.98 % ) Sampling Time: 00:43:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23362030 Comparison Time: 21:25:06 (hh:mm:ss) Elapsed Time, 1583535 HSPs Collected Number of families returned by RECON: 34275 Round Time: 22:38:52 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatScout/RECON discovery complete: 918 families found Classification Time: 00:41:47 (hh:mm:ss) Elapsed Time Program Time: 27:56:11 (hh:mm:ss) Elapsed Time