RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.BYqlUM/RM_646485.FriSep120310132025 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: 1757671812 Database = /dev/shm/rModeler.BYqlUM/GCA_032356545.1_MYCT-2423-2021 - Sequences = 350 - Bases = 14784601 - N50 = 110990 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 265441-284365 | [ 1 ] 246517-265440 | [ 2 ] 227593-246516 | [ ] 208670-227593 |* [ 4 ] 189746-208669 | [ 3 ] 170822-189745 |* [ 6 ] 151898-170821 |* [ 4 ] 132975-151898 |* [ 7 ] 114051-132974 |**** [ 17 ] 95127-114050 |*** [ 14 ] 76203-95126 |**** [ 19 ] 57280-76203 |***** [ 20 ] 38356-57279 |****** [ 26 ] 19432-38355 |******* [ 31 ] 509-19432 |************************************************** [ 196 ] Storage Throughput = excellent ( 1654.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14784558 bp ( 14701253 non ambiguous ) - Num Contigs Represented = 350 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 13, min = 10 ).. - RepeatScout: Running RepeatScout.. : 46 raw families identified - RepeatScout: Running filtering stage.. 42 families remaining - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 36 families... 00:00:27 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 3 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:33 (hh:mm:ss) Elapsed Time : 33 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 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 537 repeats masked totaling 215058 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10094004 bp Num Contigs Represented = 270 Non ambiguous bp: Initial: 10011119 bp After Masking: 9683456 bp Masked: 3.27 % -- Input Database Coverage: 10094004 bp out of 14784601 bp ( 68.27 % ) Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 87990 Comparison Time: 00:06:42 (hh:mm:ss) Elapsed Time, 4484 HSPs Collected Number of families returned by RECON: 1004 Round Time: 00:07:26 (hh:mm:ss) Elapsed Time : 2 families discovered. - Increasing sample size to include end piece now = 34784601 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34784601 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... 266 repeats masked totaling 105280 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4690549 bp Num Contigs Represented = 152 Non ambiguous bp: Initial: 4690129 bp After Masking: 4530583 bp Masked: 3.40 % -- Input Database Coverage: 14784553 bp out of 14784601 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 18336 Comparison Time: 00:02:16 (hh:mm:ss) Elapsed Time, 784 HSPs Collected Number of families returned by RECON: 336 Round Time: 00:02:26 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 35 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.BYqlUM/RM_646485.FriSep120310132025 # 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: 00:11:35 (hh:mm:ss) Elapsed Time