RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Nx9KDs/RM_2923525.FriSep120305442025 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: 1757671543 Database = /dev/shm/rModeler.Nx9KDs/GCA_032356465.1_MYCT-2728-2021 - Sequences = 314 - Bases = 14774280 - N50 = 113684 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 445423-477203 | [ 1 ] 413643-445422 | [ ] 381863-413642 | [ ] 350083-381862 | [ ] 318303-350082 | [ 1 ] 286523-318302 | [ ] 254743-286522 | [ 1 ] 222964-254743 | [ 2 ] 191184-222963 |* [ 4 ] 159404-191183 |** [ 10 ] 127624-159403 |*** [ 12 ] 95844-127623 |******* [ 26 ] 64064-95843 |********* [ 33 ] 32284-64063 |*********** [ 41 ] 505-32284 |************************************************** [ 183 ] Storage Throughput = excellent ( 1693.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14774185 bp ( 14755264 non ambiguous ) - Num Contigs Represented = 314 - 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.. : 57 raw families identified - RepeatScout: Running filtering stage.. 52 families remaining - RepeatScout: 00:01:03 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 41 families... 00:00:17 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 2 satellite(s), 4 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:01:23 (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 : 00:00:01 (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... 546 repeats masked totaling 194879 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10055166 bp Num Contigs Represented = 245 Non ambiguous bp: Initial: 10037014 bp After Masking: 9716479 bp Masked: 3.19 % -- Input Database Coverage: 10055166 bp out of 14774280 bp ( 68.06 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 77421 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 4016 HSPs Collected Number of families returned by RECON: 1001 Round Time: 00:06:37 (hh:mm:ss) Elapsed Time : 1 families discovered. - Increasing sample size to include end piece now = 34774280 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34774280 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 319 repeats masked totaling 123839 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4718939 bp Num Contigs Represented = 146 Non ambiguous bp: Initial: 4718170 bp After Masking: 4539661 bp Masked: 3.78 % -- Input Database Coverage: 14774105 bp out of 14774280 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 17391 Comparison Time: 00:02:28 (hh:mm:ss) Elapsed Time, 903 HSPs Collected Number of families returned by RECON: 332 Round Time: 00:02:37 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 36 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Nx9KDs/RM_2923525.FriSep120305442025 # 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: 00:00:09 (hh:mm:ss) Elapsed Time Program Time: 00:10:46 (hh:mm:ss) Elapsed Time