RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.s309rx/RM_66160.FriSep120341412025 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: 1757673701 Database = /dev/shm/rModeler.s309rx/GCA_032356885.1_MYCT-2250-2020 - Sequences = 323 - Bases = 14814971 - N50 = 110860 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 269664-288890 | [ 2 ] 250438-269663 | [ ] 231213-250438 | [ 2 ] 211987-231212 | [ 3 ] 192762-211987 |* [ 5 ] 173536-192761 | [ 3 ] 154311-173536 |* [ 6 ] 135085-154310 |*** [ 10 ] 115860-135085 |*** [ 11 ] 96634-115859 |**** [ 13 ] 77409-96634 |****** [ 21 ] 58183-77408 |******* [ 24 ] 38958-58183 |******* [ 23 ] 19732-38957 |************ [ 39 ] 507-19732 |************************************************** [ 161 ] Storage Throughput = excellent ( 1297.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 14814916 bp ( 14795188 non ambiguous ) - Num Contigs Represented = 323 - 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.. : 48 raw families identified - RepeatScout: Running filtering stage.. 44 families remaining - RepeatScout: 00:01:09 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 34 families... 00:00:21 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 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: 00:01:33 (hh:mm:ss) Elapsed Time : 29 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... 528 repeats masked totaling 214188 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10048157 bp Num Contigs Represented = 257 Non ambiguous bp: Initial: 10031865 bp After Masking: 9703679 bp Masked: 3.27 % -- Input Database Coverage: 10048157 bp out of 14814971 bp ( 67.82 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 80601 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 3737 HSPs Collected Number of families returned by RECON: 1029 Round Time: 00:06:47 (hh:mm:ss) Elapsed Time : 3 families discovered. - Increasing sample size to include end piece now = 34814971 RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 34814971 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... 380 repeats masked totaling 143144 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4766679 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 4763243 bp After Masking: 4571853 bp Masked: 4.02 % -- Input Database Coverage: 14814836 bp out of 14814971 bp ( 100.00 % ) Sampling Time: 00:00:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 17578 Comparison Time: 00:02:22 (hh:mm:ss) Elapsed Time, 729 HSPs Collected Number of families returned by RECON: 306 Round Time: 00:02:32 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 32 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.s309rx/RM_66160.FriSep120341412025 # 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: 00:00:07 (hh:mm:ss) Elapsed Time Program Time: 00:10:59 (hh:mm:ss) Elapsed Time