RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.OBnhEh/RM_4068850.FriSep122101582025 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: 1757736117 Database = /dev/shm/rModeler.OBnhEh/GCA_051397755.1_GA15_5 - Sequences = 680 - Bases = 40536102 - N50 = 211643 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 884092-947206 | [ 1 ] 820978-884091 | [ 1 ] 757864-820977 | [ ] 694751-757864 | [ ] 631637-694750 | [ 1 ] 568523-631636 | [ ] 505409-568522 | [ 3 ] 442296-505409 | [ 3 ] 379182-442295 | [ 9 ] 316068-379181 |* [ 12 ] 252954-316067 | [ 10 ] 189841-252954 |*** [ 31 ] 126727-189840 |**** [ 49 ] 63613-126726 |***** [ 56 ] 500-63613 |************************************************** [ 504 ] Storage Throughput = excellent ( 1754.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036991 bp ( 40036072 non ambiguous ) - Num Contigs Represented = 674 - 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.. : 49 raw families identified - RepeatScout: Running filtering stage.. 48 families remaining - RepeatScout: 00:00:43 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 43 families... 00:00:09 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 8 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:57 (hh:mm:ss) Elapsed Time : 35 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 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 372 repeats masked totaling 95000 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025568 bp Num Contigs Represented = 265 Non ambiguous bp: Initial: 10025338 bp After Masking: 9907672 bp Masked: 1.17 % -- Input Database Coverage: 10025568 bp out of 40536102 bp ( 24.73 % ) Sampling Time: 00:00:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 70500 Comparison Time: 00:04:23 (hh:mm:ss) Elapsed Time, 2239 HSPs Collected Number of families returned by RECON: 874 Round Time: 00:04:36 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1201 repeats masked totaling 361348 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011343 bp Num Contigs Represented = 556 Non ambiguous bp: Initial: 30010654 bp After Masking: 29565833 bp Masked: 1.48 % -- Input Database Coverage: 40036911 bp out of 40536102 bp ( 98.77 % ) Sampling Time: 00:00:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 632250 Comparison Time: 00:17:38 (hh:mm:ss) Elapsed Time, 18770 HSPs Collected Number of families returned by RECON: 3942 Round Time: 00:18:33 (hh:mm:ss) Elapsed Time : 21 families discovered. - Increasing sample size to include end piece now = 90510534 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90510534 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25 repeats masked totaling 5418 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 498969 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 498945 bp After Masking: 490442 bp Masked: 1.70 % -- Input Database Coverage: 40535880 bp out of 40536102 bp ( 100.00 % ) Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 171 Comparison Time: 00:00:11 (hh:mm:ss) Elapsed Time, 0 HSPs Collected Round Time: 00:00:14 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 57 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.OBnhEh/RM_4068850.FriSep122101582025 # 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: 00:24:30 (hh:mm:ss) Elapsed Time