RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.bt5cy4/RM_1318278.TueJun231515312026 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: 1782252928 Database = /dev/shm/rModeler.bt5cy4/GCF_963971535.1_fNotCoa1.1 - Sequences = 5982 - Bases = 3427786127 - N50 = 182226839 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 301738038-323290686 | [ 1 ] 280185391-301738038 | [ ] 258632744-280185391 | [ ] 237080097-258632744 | [ ] 215527450-237080097 | [ 1 ] 193974803-215527450 | [ 3 ] 172422156-193974803 | [ 2 ] 150869508-172422155 | [ 2 ] 129316861-150869508 | [ 3 ] 107764214-129316861 | [ 5 ] 86211567-107764214 | [ 2 ] 64658920-86211567 | [ 1 ] 43106273-64658920 | [ ] 21553626-43106273 | [ ] 979-21553626 |************************************************** [ 5962 ] Storage Throughput = excellent ( 1650.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40060724 bp ( 40023896 non ambiguous ) - Num Contigs Represented = 144 - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 1527 raw families identified - RepeatScout: Running filtering stage.. 1337 families remaining - RepeatScout: 00:05:49 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 1313 families... 00:14:14 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 11 satellite(s), 535 contained, found in 00:00:08 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:09 (hh:mm:ss) Elapsed Time Round Time: 00:21:33 (hh:mm:ss) Elapsed Time : 772 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18289 repeats masked totaling 5239815 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022906 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10013112 bp After Masking: 3167792 bp Masked: 68.36 % -- Input Database Coverage: 10022906 bp out of 3427786127 bp ( 0.29 % ) Sampling Time: 00:02:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 30409 HSPs Collected Number of families returned by RECON: 1532 Round Time: 00:06:18 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56816 repeats masked totaling 16453655 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037738 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 30010704 bp After Masking: 9181320 bp Masked: 69.41 % -- Input Database Coverage: 40060644 bp out of 3427786127 bp ( 1.17 % ) Sampling Time: 00:06:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 306936 Comparison Time: 00:11:33 (hh:mm:ss) Elapsed Time, 72159 HSPs Collected Number of families returned by RECON: 4504 Round Time: 00:18:56 (hh:mm:ss) Elapsed Time : 126 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 180922 repeats masked totaling 51310318 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90104902 bp Num Contigs Represented = 308 Non ambiguous bp: Initial: 90026739 bp After Masking: 25479103 bp Masked: 71.70 % -- Input Database Coverage: 130165546 bp out of 3427786127 bp ( 3.80 % ) Sampling Time: 00:17:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2755378 Comparison Time: 00:50:45 (hh:mm:ss) Elapsed Time, 370971 HSPs Collected Number of families returned by RECON: 10535 Round Time: 01:13:49 (hh:mm:ss) Elapsed Time : 666 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 621106 repeats masked totaling 174806591 bp(s). - TE Masking time 00:12:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270241663 bp Num Contigs Represented = 731 Non ambiguous bp: Initial: 270001945 bp After Masking: 57205289 bp Masked: 78.81 % -- Input Database Coverage: 400407209 bp out of 3427786127 bp ( 11.68 % ) Sampling Time: 01:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24545521 Comparison Time: 04:07:22 (hh:mm:ss) Elapsed Time, 1042918 HSPs Collected Number of families returned by RECON: 20912 Round Time: 05:24:45 (hh:mm:ss) Elapsed Time : 1538 families discovered. RepeatScout/RECON discovery complete: 3128 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.bt5cy4/RM_1318278.TueJun231515312026 # 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: 00:07:57 (hh:mm:ss) Elapsed Time Program Time: 07:33:18 (hh:mm:ss) Elapsed Time