RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.rbM71T/RM_862713.FriSep120326572025 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: 1757672816 Database = /dev/shm/rModeler.rbM71T/GCA_032356725.1_MYCT-1405-2021 - Sequences = 395 - Bases = 14817423 - N50 = 88865 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 295896-316996 | [ 1 ] 274796-295895 | [ 1 ] 253697-274796 | [ ] 232597-253696 | [ ] 211498-232597 | [ 1 ] 190398-211497 | [ 2 ] 169299-190398 | [ 1 ] 148199-169298 |* [ 6 ] 127100-148199 |*** [ 13 ] 106000-127099 |*** [ 15 ] 84901-106000 |***** [ 24 ] 63801-84900 |***** [ 25 ] 42702-63801 |******* [ 31 ] 21602-42701 |************** [ 62 ] 503-21602 |************************************************** [ 213 ] Storage Throughput = excellent ( 1690.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14817320 bp ( 14815365 non ambiguous ) - Num Contigs Represented = 395 - 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.. : 59 raw families identified - RepeatScout: Running filtering stage.. 54 families remaining - RepeatScout: 00:01:04 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 47 families... 00:00:26 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 7 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:33 (hh:mm:ss) Elapsed Time : 39 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 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 577 repeats masked totaling 167716 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026849 bp Num Contigs Represented = 291 Non ambiguous bp: Initial: 10025388 bp After Masking: 9743844 bp Masked: 2.81 % -- Input Database Coverage: 10026849 bp out of 14817423 bp ( 67.67 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 90100 Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 4272 HSPs Collected Number of families returned by RECON: 1006 Round Time: 00:06:39 (hh:mm:ss) Elapsed Time : 4 families discovered. - Increasing sample size to include end piece now = 34817423 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34817423 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 464 repeats masked totaling 153132 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4790391 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 4789897 bp After Masking: 4580830 bp Masked: 4.36 % -- Input Database Coverage: 14817240 bp out of 14817423 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 21736 Comparison Time: 00:02:20 (hh:mm:ss) Elapsed Time, 722 HSPs Collected Number of families returned by RECON: 305 Round Time: 00:02:29 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 43 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.rbM71T/RM_862713.FriSep120326572025 # 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: 00:00:07 (hh:mm:ss) Elapsed Time Program Time: 00:10:48 (hh:mm:ss) Elapsed Time