RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.DgacmI/RM_2043606.FriSep120306422025 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: 1757671601 Database = /dev/shm/rModeler.DgacmI/GCA_032356485.1_MYCT-0644-2021 - Sequences = 331 - Bases = 14789343 - N50 = 103687 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 393486-421557 | [ 1 ] 365416-393486 | [ ] 337345-365415 | [ 1 ] 309275-337345 | [ ] 281204-309274 | [ 2 ] 253134-281204 | [ 3 ] 225063-253133 | [ 1 ] 196993-225063 |* [ 4 ] 168922-196992 |* [ 4 ] 140852-168922 |* [ 5 ] 112781-140851 |**** [ 16 ] 84711-112781 |***** [ 20 ] 56640-84710 |********* [ 36 ] 28570-56640 |************ [ 48 ] 500-28570 |************************************************** [ 190 ] Storage Throughput = excellent ( 1760.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14789284 bp ( 14786612 non ambiguous ) - Num Contigs Represented = 331 - 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.. : 52 raw families identified - RepeatScout: Running filtering stage.. 48 families remaining - RepeatScout: 00:01:05 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 38 families... 00:00:30 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 2 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:38 (hh:mm:ss) Elapsed Time : 35 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... 620 repeats masked totaling 229956 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007160 bp Num Contigs Represented = 255 Non ambiguous bp: Initial: 10005705 bp After Masking: 9658452 bp Masked: 3.47 % -- Input Database Coverage: 10007160 bp out of 14789343 bp ( 67.66 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 83436 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 4274 HSPs Collected Number of families returned by RECON: 1010 Round Time: 00:06:40 (hh:mm:ss) Elapsed Time : 3 families discovered. - Increasing sample size to include end piece now = 34789343 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34789343 bp - Sequence extraction : 00:00:01 (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... 279 repeats masked totaling 125703 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4782044 bp Num Contigs Represented = 145 Non ambiguous bp: Initial: 4780827 bp After Masking: 4611612 bp Masked: 3.54 % -- Input Database Coverage: 14789204 bp out of 14789343 bp ( 100.00 % ) Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 16836 Comparison Time: 00:02:31 (hh:mm:ss) Elapsed Time, 732 HSPs Collected Number of families returned by RECON: 298 Round Time: 00:02:43 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 38 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.DgacmI/RM_2043606.FriSep120306422025 # 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: 00:00:10 (hh:mm:ss) Elapsed Time Program Time: 00:11:11 (hh:mm:ss) Elapsed Time