RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Vfsz3v/RM_946398.FriSep120921262025 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: 1757694086 Database = /dev/shm/rModeler.Vfsz3v/GCA_040807145.1_ASM4080714v1 - Sequences = 16636 - Bases = 18181348 - N50 = 1173 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 12298-13141 | [ 3 ] 11455-12297 | [ 1 ] 10612-11454 | [ 1 ] 9770-10612 | [ 2 ] 8927-9769 | [ 2 ] 8084-8926 | [ 6 ] 7241-8083 | [ 7 ] 6399-7241 | [ 21 ] 5556-6398 | [ 23 ] 4713-5555 | [ 32 ] 3870-4712 | [ 58 ] 3028-3870 | [ 183 ] 2185-3027 |** [ 631 ] 1342-2184 |********** [ 2649 ] 500-1342 |************************************************** [ 13017 ] 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 ( 1718.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 18181259 bp ( 18181082 non ambiguous ) - Num Contigs Represented = 16636 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 58 raw families identified - RepeatScout: Running filtering stage.. 58 families remaining - RepeatScout: 00:00:40 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 54 families... 00:00:08 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 10 contained, found in 00:00:00 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:00 (hh:mm:ss) Elapsed Time Round Time: 00:00:53 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:00 (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... 1195 repeats masked totaling 194950 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000878 bp Num Contigs Represented = 9188 Non ambiguous bp: Initial: 10000783 bp After Masking: 9767896 bp Masked: 2.33 % -- Input Database Coverage: 10000878 bp out of 18181348 bp ( 55.01 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 42205078 Comparison Time: 00:39:56 (hh:mm:ss) Elapsed Time, 16101 HSPs Collected Number of families returned by RECON: 3142 Round Time: 00:40:39 (hh:mm:ss) Elapsed Time : 23 families discovered. - Increasing sample size to include end piece now = 38181348 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 38181348 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1806 repeats masked totaling 329419 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 8180328 bp Num Contigs Represented = 7448 Non ambiguous bp: Initial: 8180246 bp After Masking: 7817828 bp Masked: 4.43 % -- Input Database Coverage: 18181206 bp out of 18181348 bp ( 100.00 % ) Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27732628 Comparison Time: 00:31:00 (hh:mm:ss) Elapsed Time, 6947 HSPs Collected Number of families returned by RECON: 2306 Round Time: 00:31:25 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatScout/RECON discovery complete: 70 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Vfsz3v/RM_946398.FriSep120921262025 # 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: 01:13:07 (hh:mm:ss) Elapsed Time