RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.wTqejN/RM_809154.WedSep101410542025 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: 1757538653 Database = /dev/shm/rModeler.wTqejN/GCA_018154395.1_ASM1815439v1 - Sequences = 296 - Bases = 19510621 - N50 = 446481 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1741834-1866237 | [ 1 ] 1617432-1741834 | [ ] 1493029-1617431 | [ 1 ] 1368627-1493029 | [ ] 1244224-1368626 | [ ] 1119822-1244224 | [ ] 995419-1119821 | [ ] 871017-995419 | [ 1 ] 746614-871016 | [ 1 ] 622212-746614 | [ 1 ] 497809-622211 | [ 5 ] 373407-497809 |* [ 7 ] 249004-373406 |** [ 13 ] 124602-249004 |** [ 15 ] 200-124602 |************************************************** [ 251 ] Storage Throughput = excellent ( 1698.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 19510551 bp ( 19506053 non ambiguous ) - Num Contigs Represented = 296 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 24 raw families identified - RepeatScout: Running filtering stage.. 23 families remaining - RepeatScout: 00:00:26 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 21 families... 00:00:04 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:33 (hh:mm:ss) Elapsed Time : 17 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 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 341 repeats masked totaling 63312 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015914 bp Num Contigs Represented = 174 Non ambiguous bp: Initial: 10013642 bp After Masking: 9893575 bp Masked: 1.20 % -- Input Database Coverage: 10015914 bp out of 19510621 bp ( 51.34 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 71631 Comparison Time: 00:04:33 (hh:mm:ss) Elapsed Time, 19922 HSPs Collected Number of families returned by RECON: 1589 Round Time: 00:05:13 (hh:mm:ss) Elapsed Time : 6 families discovered. - Increasing sample size to include end piece now = 39510621 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 39510621 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3076 repeats masked totaling 306158 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 9494593 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 9492367 bp After Masking: 9135732 bp Masked: 3.76 % -- Input Database Coverage: 19510507 bp out of 19510621 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 67161 Comparison Time: 00:04:18 (hh:mm:ss) Elapsed Time, 2008 HSPs Collected Number of families returned by RECON: 669 Round Time: 00:04:33 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatScout/RECON discovery complete: 25 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.wTqejN/RM_809154.WedSep101410542025 # 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: 00:00:05 (hh:mm:ss) Elapsed Time Program Time: 00:10:24 (hh:mm:ss) Elapsed Time