RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.NhwuUr/RM_4078071.FriSep121726432025 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: 1757723202 Database = /data/tmp/rModeler.NhwuUr/GCA_050230425.1_ASM5023042v1 - Sequences = 7559 - Bases = 13449397 - N50 = 2469 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 22561-24137 | [ 2 ] 20985-22560 | [ ] 19409-20984 | [ ] 17833-19408 | [ ] 16258-17833 | [ 4 ] 14682-16257 | [ 6 ] 13106-14681 | [ 4 ] 11530-13105 | [ 19 ] 9954-11529 | [ 23 ] 8379-9954 | [ 50 ] 6803-8378 | [ 75 ] 5227-6802 |* [ 167 ] 3651-5226 |*** [ 406 ] 2075-3650 |********** [ 1164 ] 500-2075 |************************************************** [ 5639 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = excellent ( 1343.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 13449335 bp ( 13431889 non ambiguous ) - Num Contigs Represented = 7559 - 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.. : 21 raw families identified - RepeatScout: Running filtering stage.. 21 families remaining - RepeatScout: 00:02:01 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 18 families... 00:00:13 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 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: 00:02:19 (hh:mm:ss) Elapsed Time : 16 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 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 392 repeats masked totaling 142306 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012670 bp Num Contigs Represented = 5625 Non ambiguous bp: Initial: 10000377 bp After Masking: 9823852 bp Masked: 1.77 % -- Input Database Coverage: 10012670 bp out of 13449397 bp ( 74.45 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 15817500 Comparison Time: 00:26:39 (hh:mm:ss) Elapsed Time, 6638 HSPs Collected Number of families returned by RECON: 2709 Round Time: 00:27:27 (hh:mm:ss) Elapsed Time : 3 families discovered. - Increasing sample size to include end piece now = 33449397 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 33449397 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... 134 repeats masked totaling 41418 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3436610 bp Num Contigs Represented = 1934 Non ambiguous bp: Initial: 3431457 bp After Masking: 3378794 bp Masked: 1.53 % -- Input Database Coverage: 13449280 bp out of 13449397 bp ( 100.00 % ) Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1869211 Comparison Time: 00:08:14 (hh:mm:ss) Elapsed Time, 667 HSPs Collected Number of families returned by RECON: 418 Round Time: 00:08:27 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 19 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.NhwuUr/RM_4078071.FriSep121726432025 # 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: 00:00:12 (hh:mm:ss) Elapsed Time Program Time: 00:38:25 (hh:mm:ss) Elapsed Time