RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.dLMTnh/RM_2292919.TueJun160703562026 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1781618635 Database = /dev/shm/rModeler.dLMTnh/GCF_963513975.1_bFriCoe1.1 - Sequences = 459 - Bases = 1209226962 - N50 = 73426979 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 143234258-153465205 | [ 1 ] 133003311-143234258 | [ ] 122772364-133003311 | [ ] 112541417-122772364 | [ 2 ] 102310470-112541417 | [ ] 92079523-102310470 | [ ] 81848576-92079523 | [ 1 ] 71617629-81848576 | [ 2 ] 61386682-71617629 | [ 1 ] 51155735-61386682 | [ ] 40924788-51155735 | [ ] 30693841-40924788 | [ 3 ] 20462894-30693841 | [ 5 ] 10231947-20462894 | [ 8 ] 1000-10231947 |************************************************* [ 436 ] Storage Throughput = excellent ( 1704.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018865 bp ( 40015665 non ambiguous ) - Num Contigs Represented = 114 - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 161 raw families identified - RepeatScout: Running filtering stage.. 137 families remaining - RepeatScout: 00:04:15 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 126 families... 01:20:37 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 4 satellite(s), 42 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 01:25:28 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3098 repeats masked totaling 704405 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023592 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10022192 bp After Masking: 8376869 bp Masked: 16.42 % -- Input Database Coverage: 10023592 bp out of 1209226962 bp ( 0.83 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:04:13 (hh:mm:ss) Elapsed Time, 12238 HSPs Collected Number of families returned by RECON: 225 Round Time: 00:05:01 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9394 repeats masked totaling 2323736 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035270 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 30033470 bp After Masking: 25386858 bp Masked: 15.47 % -- Input Database Coverage: 40058862 bp out of 1209226962 bp ( 3.31 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:20:50 (hh:mm:ss) Elapsed Time, 99764 HSPs Collected Number of families returned by RECON: 1462 Round Time: 00:23:00 (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 : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29614 repeats masked totaling 6421993 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023078 bp Num Contigs Represented = 171 Non ambiguous bp: Initial: 90013278 bp After Masking: 76187315 bp Masked: 15.36 % -- Input Database Coverage: 130081940 bp out of 1209226962 bp ( 10.76 % ) Sampling Time: 00:06:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:06:15 (hh:mm:ss) Elapsed Time, 925615 HSPs Collected Number of families returned by RECON: 9426 Round Time: 02:16:01 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 126005 repeats masked totaling 26804894 bp(s). - TE Masking time 00:04:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051930 bp Num Contigs Represented = 299 Non ambiguous bp: Initial: 270028730 bp After Masking: 220490731 bp Masked: 18.35 % -- Input Database Coverage: 400133870 bp out of 1209226962 bp ( 33.09 % ) Sampling Time: 00:19:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 14:00:04 (hh:mm:ss) Elapsed Time, 8320543 HSPs Collected Number of families returned by RECON: 57606 Round Time: 14:35:59 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatScout/RECON discovery complete: 404 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.dLMTnh/RM_2292919.TueJun160703562026 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:02:23 (hh:mm:ss) Elapsed Time Program Time: 18:47:52 (hh:mm:ss) Elapsed Time