RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.ZTSNwY/RM_806306.TueSep92043452025 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: 1757475824 Database = /dev/shm/rModeler.ZTSNwY/GCA_011764045.1_ASM1176404v1 - Sequences = 52660 - Bases = 47748369 - N50 = 3771 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 172862-185196 | [ 1 ] 160529-172862 | [ ] 148196-160529 | [ 1 ] 135863-148196 | [ ] 123530-135863 | [ ] 111197-123530 | [ 4 ] 98864-111197 | [ 4 ] 86531-98864 | [ 7 ] 74198-86531 | [ 6 ] 61865-74198 | [ 18 ] 49532-61865 | [ 43 ] 37199-49532 | [ 84 ] 24866-37199 | [ 161 ] 12533-24866 | [ 312 ] 200-12533 |************************************************* [ 52019 ] 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 ( 1175.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001860 bp ( 39999980 non ambiguous ) - Num Contigs Represented = 44381 - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 307 raw families identified - RepeatScout: Running filtering stage.. 298 families remaining - RepeatScout: 00:03:26 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 284 families... 00:00:49 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 65 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:04:31 (hh:mm:ss) Elapsed Time : 219 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 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2738 repeats masked totaling 621409 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001444 bp Num Contigs Represented = 11564 Non ambiguous bp: Initial: 10000781 bp After Masking: 9355522 bp Masked: 6.45 % -- Input Database Coverage: 10001444 bp out of 47748369 bp ( 20.95 % ) Sampling Time: 00:00:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 66903528 Comparison Time: 00:51:02 (hh:mm:ss) Elapsed Time, 9189 HSPs Collected Number of families returned by RECON: 2827 Round Time: 00:51:59 (hh:mm:ss) Elapsed Time : 8 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 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9104 repeats masked totaling 2078697 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001692 bp Num Contigs Represented = 32869 Non ambiguous bp: Initial: 30000475 bp After Masking: 27851336 bp Masked: 7.16 % -- Input Database Coverage: 40003136 bp out of 47748369 bp ( 83.78 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 542801826 Comparison Time: 02:43:21 (hh:mm:ss) Elapsed Time, 55388 HSPs Collected Number of families returned by RECON: 13510 Round Time: 02:49:19 (hh:mm:ss) Elapsed Time : 83 families discovered. - Increasing sample size to include end piece now = 97746925 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 97746925 bp - Sequence extraction : 00:00:02 (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... 3122 repeats masked totaling 735809 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 7745049 bp Num Contigs Represented = 8316 Non ambiguous bp: Initial: 7744534 bp After Masking: 6992786 bp Masked: 9.71 % -- Input Database Coverage: 47748185 bp out of 47748369 bp ( 100.00 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34623681 Comparison Time: 00:34:44 (hh:mm:ss) Elapsed Time, 2650 HSPs Collected Number of families returned by RECON: 1564 Round Time: 00:35:27 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatScout/RECON discovery complete: 311 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.ZTSNwY/RM_806306.TueSep92043452025 # 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: 00:01:19 (hh:mm:ss) Elapsed Time Program Time: 04:22:35 (hh:mm:ss) Elapsed Time