RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.XLUIJg/RM_2194249.SatSep130322432025 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: 1757758963 Database = /dev/shm/rModeler.XLUIJg/GCA_900155495.1_Tinctoporellus_epimiltinus_RS1 - Sequences = 2002 - Bases = 46180263 - N50 = 58956 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206772-221470 | [ 3 ] 192074-206771 | [ 4 ] 177376-192073 | [ 2 ] 162678-177375 | [ 8 ] 147980-162677 | [ 8 ] 133282-147979 | [ 6 ] 118584-133281 | [ 19 ] 103886-118583 | [ 23 ] 89188-103885 |* [ 46 ] 74490-89187 |* [ 46 ] 59792-74489 |** [ 68 ] 45094-59791 |*** [ 88 ] 30396-45093 |******* [ 181 ] 15698-30395 |********** [ 261 ] 1001-15698 |************************************************** [ 1239 ] Storage Throughput = excellent ( 1763.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045078 bp ( 40041209 non ambiguous ) - Num Contigs Represented = 1779 - 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.. : 260 raw families identified - RepeatScout: Running filtering stage.. 257 families remaining - RepeatScout: 00:01:06 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 254 families... 00:00:35 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 66 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:47 (hh:mm:ss) Elapsed Time : 188 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 00:00:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1662 repeats masked totaling 796369 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041847 bp Num Contigs Represented = 495 Non ambiguous bp: Initial: 10041064 bp After Masking: 9228735 bp Masked: 8.09 % -- Input Database Coverage: 10041847 bp out of 46180263 bp ( 21.74 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 144453 Comparison Time: 00:05:09 (hh:mm:ss) Elapsed Time, 3451 HSPs Collected Number of families returned by RECON: 1021 Round Time: 00:05:52 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5446 repeats masked totaling 2512387 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003198 bp Num Contigs Represented = 1427 Non ambiguous bp: Initial: 30000112 bp After Masking: 27440150 bp Masked: 8.53 % -- Input Database Coverage: 40045045 bp out of 46180263 bp ( 86.71 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1456071 Comparison Time: 00:22:30 (hh:mm:ss) Elapsed Time, 29929 HSPs Collected Number of families returned by RECON: 4176 Round Time: 00:23:46 (hh:mm:ss) Elapsed Time : 33 families discovered. - Increasing sample size to include end piece now = 96138416 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 96138416 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1266 repeats masked totaling 567703 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 6135040 bp Num Contigs Represented = 323 Non ambiguous bp: Initial: 6134483 bp After Masking: 5559873 bp Masked: 9.37 % -- Input Database Coverage: 46180085 bp out of 46180263 bp ( 100.00 % ) Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 56616 Comparison Time: 00:03:02 (hh:mm:ss) Elapsed Time, 922 HSPs Collected Number of families returned by RECON: 448 Round Time: 00:03:17 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 224 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.XLUIJg/RM_2194249.SatSep130322432025 # 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: 00:00:25 (hh:mm:ss) Elapsed Time Program Time: 00:35:07 (hh:mm:ss) Elapsed Time