RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.qI6tyw/RM_3630611.FriSep120318442025 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: 1757672323 Database = /data/tmp/rModeler.qI6tyw/GCA_032356585.1_MYCT-1957-2021 - Sequences = 363 - Bases = 14805871 - N50 = 98024 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 292331-313176 | [ 2 ] 271486-292330 | [ ] 250641-271485 | [ 2 ] 229797-250641 | [ 3 ] 208952-229796 | [ 1 ] 188107-208951 | [ 2 ] 167262-188106 |* [ 5 ] 146418-167262 |* [ 4 ] 125573-146417 |** [ 9 ] 104728-125572 |*** [ 14 ] 83883-104727 |**** [ 17 ] 63039-83883 |******* [ 28 ] 42194-63038 |******** [ 33 ] 21349-42193 |************ [ 49 ] 505-21349 |************************************************** [ 194 ] Storage Throughput = fair ( 660.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14805805 bp ( 14766644 non ambiguous ) - Num Contigs Represented = 363 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 13, min = 10 ).. - RepeatScout: Running RepeatScout.. : 55 raw families identified - RepeatScout: Running filtering stage.. 51 families remaining - RepeatScout: 00:02:18 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 37 families... 00:00:48 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:03:11 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 490 repeats masked totaling 242112 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10071457 bp Num Contigs Represented = 278 Non ambiguous bp: Initial: 10032836 bp After Masking: 9662419 bp Masked: 3.69 % -- Input Database Coverage: 10071457 bp out of 14805871 bp ( 68.02 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 86320 Comparison Time: 00:11:26 (hh:mm:ss) Elapsed Time, 4144 HSPs Collected Number of families returned by RECON: 1055 Round Time: 00:12:51 (hh:mm:ss) Elapsed Time : 1 families discovered. - Increasing sample size to include end piece now = 34805871 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34805871 bp - Sequence extraction : 00:00:00 (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... 322 repeats masked totaling 128099 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4734268 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 4733728 bp After Masking: 4554535 bp Masked: 3.79 % -- Input Database Coverage: 14805725 bp out of 14805871 bp ( 100.00 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 19701 Comparison Time: 00:04:11 (hh:mm:ss) Elapsed Time, 701 HSPs Collected Number of families returned by RECON: 289 Round Time: 00:04:35 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 35 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.qI6tyw/RM_3630611.FriSep120318442025 # 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: 00:00:20 (hh:mm:ss) Elapsed Time Program Time: 00:20:57 (hh:mm:ss) Elapsed Time