RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.6RU398/RM_1044509.FriSep120340112025 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: 1757673611 Database = /dev/shm/rModeler.6RU398/GCA_032356865.1_MYCT-2012-2020 - Sequences = 394 - Bases = 14711221 - N50 = 92168 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 280340-300329 | [ 2 ] 260352-280340 | [ 1 ] 240363-260351 | [ ] 220375-240363 | [ ] 200387-220375 | [ 2 ] 180398-200386 | [ 3 ] 160410-180398 | [ 2 ] 140421-160409 |* [ 7 ] 120433-140421 |* [ 7 ] 100445-120433 |**** [ 19 ] 80456-100444 |***** [ 21 ] 60468-80456 |***** [ 23 ] 40479-60467 |********** [ 42 ] 20491-40479 |************** [ 61 ] 503-20491 |************************************************** [ 204 ] Storage Throughput = excellent ( 1627.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14711153 bp ( 14708138 non ambiguous ) - Num Contigs Represented = 394 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 13, min = 10 ).. - RepeatScout: Running RepeatScout.. : 46 raw families identified - RepeatScout: Running filtering stage.. 39 families remaining - RepeatScout: 00:01:02 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 36 families... 00:00:15 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 5 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:20 (hh:mm:ss) Elapsed Time : 31 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 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 523 repeats masked totaling 231363 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011672 bp Num Contigs Represented = 320 Non ambiguous bp: Initial: 10010283 bp After Masking: 9662938 bp Masked: 3.47 % -- Input Database Coverage: 10011672 bp out of 14711221 bp ( 68.05 % ) Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 99681 Comparison Time: 00:06:40 (hh:mm:ss) Elapsed Time, 4543 HSPs Collected Number of families returned by RECON: 1066 Round Time: 00:07:13 (hh:mm:ss) Elapsed Time : 2 families discovered. - Increasing sample size to include end piece now = 34711221 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34711221 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 264 repeats masked totaling 124677 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4699401 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 4697775 bp After Masking: 4533537 bp Masked: 3.50 % -- Input Database Coverage: 14711073 bp out of 14711221 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 17391 Comparison Time: 00:02:20 (hh:mm:ss) Elapsed Time, 665 HSPs Collected Number of families returned by RECON: 312 Round Time: 00:02:29 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 33 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.6RU398/RM_1044509.FriSep120340112025 # 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: 00:00:08 (hh:mm:ss) Elapsed Time Program Time: 00:11:10 (hh:mm:ss) Elapsed Time