RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.5veCBu/RM_3278352.SatSep130123422025 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: 1757751821 Database = /dev/shm/rModeler.5veCBu/GCA_051944405.1_ASM5194440v1 - Sequences = 7760 - Bases = 13954474 - N50 = 6400 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 73260-78479 | [ 3 ] 68041-73259 | [ 2 ] 62823-68041 | [ 4 ] 57604-62822 | [ 3 ] 52386-57604 | [ 5 ] 47167-52385 | [ 5 ] 41948-47166 | [ 7 ] 36730-41948 | [ 7 ] 31511-36729 | [ 13 ] 26293-31511 | [ 17 ] 21074-26292 | [ 25 ] 15855-21073 | [ 36 ] 10637-15855 | [ 97 ] 5418-10636 |* [ 282 ] 200-5418 |************************************************* [ 7254 ] 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 ( 1657.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 13954369 bp ( 13908617 non ambiguous ) - Num Contigs Represented = 7760 - 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.. : 22 raw families identified - RepeatScout: Running filtering stage.. 22 families remaining - RepeatScout: 00:01:00 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 21 families... 00:00:05 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 5 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 : 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 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 337 repeats masked totaling 72132 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10044850 bp Num Contigs Represented = 5586 Non ambiguous bp: Initial: 10013272 bp After Masking: 9895830 bp Masked: 1.17 % -- Input Database Coverage: 10044850 bp out of 13954474 bp ( 71.98 % ) Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 15671601 Comparison Time: 00:23:10 (hh:mm:ss) Elapsed Time, 6298 HSPs Collected Number of families returned by RECON: 2805 Round Time: 00:23:40 (hh:mm:ss) Elapsed Time : 5 families discovered. - Increasing sample size to include end piece now = 33954474 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 33954474 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 163 repeats masked totaling 41257 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 3909447 bp Num Contigs Represented = 2191 Non ambiguous bp: Initial: 3895273 bp After Masking: 3838299 bp Masked: 1.46 % -- Input Database Coverage: 13954297 bp out of 13954474 bp ( 100.00 % ) Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2401336 Comparison Time: 00:08:24 (hh:mm:ss) Elapsed Time, 914 HSPs Collected Number of families returned by RECON: 556 Round Time: 00:08:31 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 21 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.5veCBu/RM_3278352.SatSep130123422025 # 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: 00:00:06 (hh:mm:ss) Elapsed Time Program Time: 00:33:25 (hh:mm:ss) Elapsed Time