RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.A1qQHb/RM_1897105.MonSep81700002025 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: 1757376000 Database = /dev/shm/rModeler.A1qQHb/GCA_002196585.2_FUS01-V2 - Sequences = 881 - Bases = 49057912 - N50 = 842521 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 4583191-4910526 | [ 1 ] 4255856-4583190 | [ ] 3928521-4255855 | [ ] 3601186-3928520 | [ ] 3273851-3601185 | [ ] 2946516-3273850 | [ ] 2619181-2946515 | [ ] 2291846-2619180 | [ ] 1964511-2291845 | [ 2 ] 1637176-1964510 | [ 1 ] 1309841-1637175 | [ 3 ] 982506-1309840 | [ 4 ] 655171-982505 | [ 12 ] 327836-655170 | [ 16 ] 502-327836 |************************************************** [ 842 ] Storage Throughput = excellent ( 1576.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017185 bp ( 40016922 non ambiguous ) - Num Contigs Represented = 723 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 66 raw families identified - RepeatScout: Running filtering stage.. 48 families remaining - RepeatScout: 00:00:46 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 45 families... 00:04:40 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 8 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:05:31 (hh:mm:ss) Elapsed Time : 37 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 701 repeats masked totaling 331955 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004220 bp Num Contigs Represented = 237 Non ambiguous bp: Initial: 10004163 bp After Masking: 9646593 bp Masked: 3.57 % -- Input Database Coverage: 10004220 bp out of 49057912 bp ( 20.39 % ) Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 78210 Comparison Time: 00:05:43 (hh:mm:ss) Elapsed Time, 4012 HSPs Collected Number of families returned by RECON: 881 Round Time: 00:09:38 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2235 repeats masked totaling 928191 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012888 bp Num Contigs Represented = 560 Non ambiguous bp: Initial: 30012682 bp After Masking: 29029500 bp Masked: 3.28 % -- Input Database Coverage: 40017108 bp out of 49057912 bp ( 81.57 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 700336 Comparison Time: 00:18:45 (hh:mm:ss) Elapsed Time, 19084 HSPs Collected Number of families returned by RECON: 3757 Round Time: 00:27:15 (hh:mm:ss) Elapsed Time : 19 families discovered. - Increasing sample size to include end piece now = 99053692 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 99053692 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1012 repeats masked totaling 473550 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 9040578 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 9040467 bp After Masking: 8551921 bp Masked: 5.40 % -- Input Database Coverage: 49057686 bp out of 49057912 bp ( 100.00 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 70500 Comparison Time: 00:04:02 (hh:mm:ss) Elapsed Time, 1736 HSPs Collected Number of families returned by RECON: 613 Round Time: 00:05:11 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatScout/RECON discovery complete: 61 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.A1qQHb/RM_1897105.MonSep81700002025 # 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: 00:00:15 (hh:mm:ss) Elapsed Time Program Time: 00:47:50 (hh:mm:ss) Elapsed Time