RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.fdylcY/RM_1431404.FriNov150016282024 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: 1731658588 Database = /scratch/tmp/rModeler.fdylcY/GCA_964194105.1_mSpeCit3.1 - Sequences = 498 - Bases = 3090049053 - N50 = 166248449 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 269702567-288966967 | [ 1 ] 250438168-269702567 | [ 1 ] 231173769-250438168 | [ 2 ] 211909370-231173769 | [ ] 192644971-211909370 | [ ] 173380571-192644970 | [ 1 ] 154116172-173380571 | [ 3 ] 134851773-154116172 | [ 4 ] 115587374-134851773 | [ 2 ] 96322975-115587374 | [ 2 ] 77058575-96322974 | [ 2 ] 57794176-77058575 | [ 1 ] 38529777-57794176 | [ ] 19265378-38529777 | [ 1 ] 979-19265378 |************************************************** [ 478 ] Storage Throughput = excellent ( 1427.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041796 bp ( 40036596 non ambiguous ) - Num Contigs Represented = 69 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:57 (hh:mm:ss) Elapsed Time Round Time: 00:14:44 (hh:mm:ss) Elapsed Time : 208 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 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11229 repeats masked totaling 2405427 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10013614 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10011814 bp After Masking: 6707725 bp Masked: 33.00 % -- Input Database Coverage: 10013614 bp out of 3090049053 bp ( 0.32 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 5218 HSPs Collected Number of families returned by RECON: 665 Round Time: 00:03:56 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35254 repeats masked totaling 7327856 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028102 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30024702 bp After Masking: 19966865 bp Masked: 33.50 % -- Input Database Coverage: 40041716 bp out of 3090049053 bp ( 1.30 % ) Sampling Time: 00:02:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:15:15 (hh:mm:ss) Elapsed Time, 32035 HSPs Collected Number of families returned by RECON: 2234 Round Time: 00:17:54 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:01 (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... 112752 repeats masked totaling 23570737 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025668 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 90017677 bp After Masking: 57018271 bp Masked: 36.66 % -- Input Database Coverage: 130067384 bp out of 3090049053 bp ( 4.21 % ) Sampling Time: 00:07:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 01:19:21 (hh:mm:ss) Elapsed Time, 130810 HSPs Collected Number of families returned by RECON: 8324 Round Time: 01:28:44 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 384026 repeats masked totaling 81435853 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047875 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 270022561 bp After Masking: 159436439 bp Masked: 40.95 % -- Input Database Coverage: 400115259 bp out of 3090049053 bp ( 12.95 % ) Sampling Time: 00:22:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 08:45:24 (hh:mm:ss) Elapsed Time, 526291 HSPs Collected Number of families returned by RECON: 30184 Round Time: 09:15:41 (hh:mm:ss) Elapsed Time : 306 families discovered. RepeatScout/RECON discovery complete: 765 families found Classification Time: 00:23:22 (hh:mm:ss) Elapsed Time Program Time: 11:44:21 (hh:mm:ss) Elapsed Time