RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RYRolf/RM_592.FriJan62201422023 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: 1673071301 Database = /dev/shm/rModeler.RYRolf/GCF_009769625.2_bCygOlo1.pri.v2 - Sequences = 171 - Bases = 1134186642 - N50 = 121075659 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 195554094-209522193 | [ 1 ] 181585995-195554093 | [ ] 167617896-181585994 | [ ] 153649797-167617895 | [ 1 ] 139681699-153649797 | [ ] 125713600-139681698 | [ ] 111745501-125713599 | [ 1 ] 97777402-111745500 | [ ] 83809303-97777401 | [ ] 69841205-83809303 | [ 2 ] 55873106-69841204 | [ 1 ] 41905007-55873105 | [ ] 27936908-41905006 | [ 3 ] 13968809-27936907 |** [ 9 ] 711-13968809 |************************************************** [ 153 ] Storage Throughput = excellent ( 1136.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40323879 bp ( 40002644 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:01 (hh:mm:ss) Elapsed Time Round Time: 00:28:18 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1434 repeats masked totaling 651889 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10085711 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10037400 bp After Masking: 9297123 bp Masked: 7.38 % -- Input Database Coverage: 10085711 bp out of 1134186642 bp ( 0.89 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:47 (hh:mm:ss) Elapsed Time, 1185 HSPs Collected Number of families returned by RECON: 266 Round Time: 00:08:49 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4380 repeats masked totaling 1835974 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30278088 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30005164 bp After Masking: 27965743 bp Masked: 6.80 % -- Input Database Coverage: 40363799 bp out of 1134186642 bp ( 3.56 % ) Sampling Time: 00:02:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:45:27 (hh:mm:ss) Elapsed Time, 3652 HSPs Collected Number of families returned by RECON: 1556 Round Time: 00:48:33 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14189 repeats masked totaling 5853843 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90743123 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90026757 bp After Masking: 83606261 bp Masked: 7.13 % -- Input Database Coverage: 131106922 bp out of 1134186642 bp ( 11.56 % ) Sampling Time: 00:08:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 05:37:45 (hh:mm:ss) Elapsed Time, 31416 HSPs Collected Number of families returned by RECON: 9939 Round Time: 05:48:11 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51505 repeats masked totaling 18970038 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272333237 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 270014719 bp After Masking: 249035621 bp Masked: 7.77 % -- Input Database Coverage: 403440159 bp out of 1134186642 bp ( 35.57 % ) Sampling Time: 00:25:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 46:48:43 (hh:mm:ss) Elapsed Time, 174646 HSPs Collected Number of families returned by RECON: 63405 Round Time: 48:10:29 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatScout/RECON discovery complete: 270 families found Classification Time: 00:15:36 (hh:mm:ss) Elapsed Time Program Time: 55:39:56 (hh:mm:ss) Elapsed Time