RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4nU4Jl/RM_10933.SunOct271522412024 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: 1730067760 Database = /dev/shm/rModeler.4nU4Jl/GCA_019455555.1_Gpyr_1.0 - Sequences = 12306 - Bases = 1828347170 - N50 = 8555737 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33977670-36404611 | [ 1 ] 31550729-33977669 | [ ] 29123788-31550728 | [ ] 26696848-29123788 | [ ] 24269907-26696847 | [ 2 ] 21842966-24269906 | [ 4 ] 19416025-21842965 | [ 3 ] 16989085-19416025 | [ 4 ] 14562144-16989084 | [ 8 ] 12135203-14562143 | [ 8 ] 9708262-12135202 | [ 27 ] 7281322-9708262 | [ 17 ] 4854381-7281321 | [ 44 ] 2427440-4854380 | [ 78 ] 500-2427440 |************************************************** [ 12110 ] Storage Throughput = excellent ( 1092.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40556205 bp ( 40015617 non ambiguous ) - Num Contigs Represented = 551 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:31 (hh:mm:ss) Elapsed Time Round Time: 00:23:47 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6733 repeats masked totaling 1561620 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10108952 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 10010969 bp After Masking: 8414582 bp Masked: 15.95 % -- Input Database Coverage: 10108952 bp out of 1828347170 bp ( 0.55 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48828 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 7176 HSPs Collected Number of families returned by RECON: 879 Round Time: 00:07:05 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24053 repeats masked totaling 5542191 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30447173 bp Num Contigs Represented = 465 Non ambiguous bp: Initial: 30004568 bp After Masking: 24361085 bp Masked: 18.81 % -- Input Database Coverage: 40556125 bp out of 1828347170 bp ( 2.22 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 460320 Comparison Time: 00:35:11 (hh:mm:ss) Elapsed Time, 17935 HSPs Collected Number of families returned by RECON: 2190 Round Time: 00:37:18 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79544 repeats masked totaling 18251877 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91423367 bp Num Contigs Represented = 990 Non ambiguous bp: Initial: 90022874 bp After Masking: 71498122 bp Masked: 20.58 % -- Input Database Coverage: 131979492 bp out of 1828347170 bp ( 7.22 % ) Sampling Time: 00:04:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4094091 Comparison Time: 04:10:31 (hh:mm:ss) Elapsed Time, 71652 HSPs Collected Number of families returned by RECON: 8499 Round Time: 04:21:17 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 265828 repeats masked totaling 60779817 bp(s). - TE Masking time 00:04:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273895128 bp Num Contigs Represented = 2256 Non ambiguous bp: Initial: 270011171 bp After Masking: 208332317 bp Masked: 22.84 % -- Input Database Coverage: 405874620 bp out of 1828347170 bp ( 22.20 % ) Sampling Time: 00:14:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36487153 Comparison Time: 32:33:42 (hh:mm:ss) Elapsed Time, 215389 HSPs Collected Number of families returned by RECON: 39790 Round Time: 33:19:26 (hh:mm:ss) Elapsed Time : 313 families discovered. RepeatScout/RECON discovery complete: 663 families found Classification Time: 00:23:34 (hh:mm:ss) Elapsed Time Program Time: 39:12:27 (hh:mm:ss) Elapsed Time