RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.tCqGIo/RM_1870280.TueNov251319212025 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: 1764105556 Database = /dev/shm/rModeler.tCqGIo/GCA_025802375.1_ASM2580237v1 - Sequences = 489895 - Bases = 450652285 - N50 = 941 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 56101-60073 | [ 2 ] 52129-56100 | [ 2 ] 48158-52129 | [ ] 44186-48157 | [ ] 40215-44186 | [ ] 36243-40214 | [ ] 32272-36243 | [ ] 28300-32271 | [ 4 ] 24329-28300 | [ 3 ] 20357-24328 | [ 8 ] 16386-20357 | [ 24 ] 12414-16385 | [ 66 ] 8443-12414 | [ 268 ] 4471-8442 | [ 2071 ] 500-4471 |************************************************** [ 487447 ] 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 ( 1184.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011719 bp ( 40001059 non ambiguous ) - Num Contigs Represented = 43654 - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 805 raw families identified - RepeatScout: Running filtering stage.. 779 families remaining - RepeatScout: 00:03:41 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 756 families... 00:04:15 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 91 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:04 (hh:mm:ss) Elapsed Time Round Time: 00:08:15 (hh:mm:ss) Elapsed Time : 665 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 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14372 repeats masked totaling 2876280 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003766 bp Num Contigs Represented = 10987 Non ambiguous bp: Initial: 10000356 bp After Masking: 6987211 bp Masked: 30.13 % -- Input Database Coverage: 10003766 bp out of 450652285 bp ( 2.22 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 60351591 Comparison Time: 00:43:56 (hh:mm:ss) Elapsed Time, 37138 HSPs Collected Number of families returned by RECON: 3244 Round Time: 00:46:37 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47836 repeats masked totaling 9614433 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007887 bp Num Contigs Represented = 32667 Non ambiguous bp: Initial: 30000637 bp After Masking: 19966407 bp Masked: 33.45 % -- Input Database Coverage: 40011653 bp out of 450652285 bp ( 8.88 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 533550111 Comparison Time: 02:25:05 (hh:mm:ss) Elapsed Time, 159790 HSPs Collected Number of families returned by RECON: 9368 Round Time: 02:35:29 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 182261 repeats masked totaling 38418571 bp(s). - TE Masking time 00:05:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020709 bp Num Contigs Represented = 98074 Non ambiguous bp: Initial: 90000210 bp After Masking: 50351611 bp Masked: 44.05 % -- Input Database Coverage: 130032362 bp out of 450652285 bp ( 28.85 % ) Sampling Time: 00:08:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4809205701 Comparison Time: 09:38:08 (hh:mm:ss) Elapsed Time, 602432 HSPs Collected Number of families returned by RECON: 25082 Round Time: 10:28:08 (hh:mm:ss) Elapsed Time : 982 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 691224 repeats masked totaling 150589791 bp(s). - TE Masking time 00:36:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066697 bp Num Contigs Represented = 293213 Non ambiguous bp: Initial: 270000309 bp After Masking: 115701047 bp Masked: 57.15 % -- Input Database Coverage: 400099059 bp out of 450652285 bp ( 88.78 % ) Sampling Time: 00:48:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42987957936 Comparison Time: 44:40:27 (hh:mm:ss) Elapsed Time, 1398344 HSPs Collected Number of families returned by RECON: 67840 Round Time: 49:05:50 (hh:mm:ss) Elapsed Time : 2251 families discovered. RepeatScout/RECON discovery complete: 4263 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.tCqGIo/RM_1870280.TueNov251319212025 # 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: 00:16:55 (hh:mm:ss) Elapsed Time Program Time: 63:21:15 (hh:mm:ss) Elapsed Time