RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.cNRxEN/RM_2190036.FriSep120319112025 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: 1757672350 Database = /dev/shm/rModeler.cNRxEN/GCA_032356605.1_MYCT-2085-2021 - Sequences = 450 - Bases = 14880662 - N50 = 81437 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 295205-316256 | [ 1 ] 274155-295205 | [ ] 253105-274155 | [ ] 232055-253105 | [ ] 211005-232055 | [ ] 189954-211004 | [ 3 ] 168904-189954 | [ 3 ] 147854-168904 | [ 2 ] 126804-147854 |*** [ 17 ] 105754-126804 |* [ 9 ] 84703-105753 |*** [ 20 ] 63653-84703 |***** [ 30 ] 42603-63653 |******** [ 41 ] 21553-42603 |************** [ 73 ] 503-21553 |************************************************** [ 251 ] Storage Throughput = excellent ( 1575.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14880569 bp ( 14878032 non ambiguous ) - Num Contigs Represented = 450 - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 13, min = 10 ).. - RepeatScout: Running RepeatScout.. : 63 raw families identified - RepeatScout: Running filtering stage.. 58 families remaining - RepeatScout: 00:01:06 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 42 families... 00:00:16 (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: 00:01:24 (hh:mm:ss) Elapsed Time : 37 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 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 623 repeats masked totaling 264016 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019872 bp Num Contigs Represented = 322 Non ambiguous bp: Initial: 10018256 bp After Masking: 9639834 bp Masked: 3.78 % -- Input Database Coverage: 10019872 bp out of 14880662 bp ( 67.33 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 100576 Comparison Time: 00:06:12 (hh:mm:ss) Elapsed Time, 3748 HSPs Collected Number of families returned by RECON: 1023 Round Time: 00:06:45 (hh:mm:ss) Elapsed Time : 2 families discovered. - Increasing sample size to include end piece now = 34880662 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34880662 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 471 repeats masked totaling 166499 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4860620 bp Num Contigs Represented = 208 Non ambiguous bp: Initial: 4859699 bp After Masking: 4638093 bp Masked: 4.56 % -- Input Database Coverage: 14880492 bp out of 14880662 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 28203 Comparison Time: 00:02:35 (hh:mm:ss) Elapsed Time, 823 HSPs Collected Number of families returned by RECON: 315 Round Time: 00:02:48 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatScout/RECON discovery complete: 40 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.cNRxEN/RM_2190036.FriSep120319112025 # 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: 00:00:08 (hh:mm:ss) Elapsed Time Program Time: 00:11:05 (hh:mm:ss) Elapsed Time