RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.nzq91O/RM_1938012.FriSep121720272025 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: 1757722827 Database = /dev/shm/rModeler.nzq91O/GCA_050230375.1_ASM5023037v1 - Sequences = 6932 - Bases = 13563728 - N50 = 3035 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 24327-26029 | [ 1 ] 22625-24326 | [ 2 ] 20923-22624 | [ 2 ] 19221-20922 | [ 5 ] 17519-19220 | [ 4 ] 15817-17518 | [ 6 ] 14115-15816 | [ 9 ] 12413-14114 | [ 17 ] 10711-12412 | [ 23 ] 9009-10710 | [ 44 ] 7307-9008 |* [ 117 ] 5605-7306 |* [ 187 ] 3903-5604 |*** [ 407 ] 2201-3902 |********* [ 983 ] 500-2201 |************************************************** [ 5125 ] 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 ( 1587.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 13563632 bp ( 13547412 non ambiguous ) - Num Contigs Represented = 6932 - 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.. : 40 raw families identified - RepeatScout: Running filtering stage.. 36 families remaining - RepeatScout: 00:00:56 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 30 families... 00:00:09 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:08 (hh:mm:ss) Elapsed Time : 30 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 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482 repeats masked totaling 151377 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011281 bp Num Contigs Represented = 5146 Non ambiguous bp: Initial: 10000008 bp After Masking: 9776708 bp Masked: 2.23 % -- Input Database Coverage: 10011281 bp out of 13563728 bp ( 73.81 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 13238085 Comparison Time: 00:21:29 (hh:mm:ss) Elapsed Time, 5909 HSPs Collected Number of families returned by RECON: 2025 Round Time: 00:21:52 (hh:mm:ss) Elapsed Time : 1 families discovered. - Increasing sample size to include end piece now = 33563728 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 33563728 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 172 repeats masked totaling 55696 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3552332 bp Num Contigs Represented = 1786 Non ambiguous bp: Initial: 3547385 bp After Masking: 3470093 bp Masked: 2.18 % -- Input Database Coverage: 13563613 bp out of 13563728 bp ( 100.00 % ) Sampling Time: 00:00:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1594005 Comparison Time: 00:06:58 (hh:mm:ss) Elapsed Time, 881 HSPs Collected Number of families returned by RECON: 390 Round Time: 00:07:05 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 31 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.nzq91O/RM_1938012.FriSep121720272025 # 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: 00:30:12 (hh:mm:ss) Elapsed Time