RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.2f9ChP/RM_3852296.MonSep81242322025 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: 1757360551 Database = /dev/shm/rModeler.2f9ChP/GCA_000825725.1_Rmicro_CBS_344.29_Allpaths-LG - Sequences = 1554 - Bases = 49238270 - N50 = 53022 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 280451-300412 | [ 1 ] 260491-280451 | [ 1 ] 240531-260491 | [ ] 220571-240531 | [ 2 ] 200611-220571 | [ 3 ] 180651-200611 | [ 3 ] 160691-180651 | [ 8 ] 140731-160691 | [ 7 ] 120771-140731 |* [ 26 ] 100811-120771 |* [ 21 ] 80851-100811 |*** [ 53 ] 60891-80851 |****** [ 93 ] 40931-60891 |********** [ 168 ] 20971-40931 |************************* [ 393 ] 1011-20971 |************************************************** [ 775 ] Storage Throughput = excellent ( 1656.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43148113 bp ( 40030076 non ambiguous ) - Num Contigs Represented = 1411 - 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.. : 382 raw families identified - RepeatScout: Running filtering stage.. 380 families remaining - RepeatScout: 00:01:42 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 368 families... 00:00:44 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 89 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:02:32 (hh:mm:ss) Elapsed Time : 279 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 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3833 repeats masked totaling 1111988 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10771327 bp Num Contigs Represented = 416 Non ambiguous bp: Initial: 10011065 bp After Masking: 8871711 bp Masked: 11.38 % -- Input Database Coverage: 10771327 bp out of 49238270 bp ( 21.88 % ) Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 108345 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 9105 HSPs Collected Number of families returned by RECON: 1617 Round Time: 00:05:47 (hh:mm:ss) Elapsed Time : 5 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 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12399 repeats masked totaling 3642563 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32376759 bp Num Contigs Represented = 1147 Non ambiguous bp: Initial: 30018984 bp After Masking: 26293126 bp Masked: 12.41 % -- Input Database Coverage: 43148086 bp out of 49238270 bp ( 87.63 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1021735 Comparison Time: 00:25:19 (hh:mm:ss) Elapsed Time, 40995 HSPs Collected Number of families returned by RECON: 5996 Round Time: 00:26:50 (hh:mm:ss) Elapsed Time : 22 families discovered. - Increasing sample size to include end piece now = 98466943 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 98466943 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2609 repeats masked totaling 733255 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 6089992 bp Num Contigs Represented = 247 Non ambiguous bp: Initial: 5597067 bp After Masking: 4848441 bp Masked: 13.38 % -- Input Database Coverage: 49238078 bp out of 49238270 bp ( 100.00 % ) Sampling Time: 00:00:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 1309 HSPs Collected Number of families returned by RECON: 658 Round Time: 00:03:03 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 306 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.2f9ChP/RM_3852296.MonSep81242322025 # 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: 00:00:36 (hh:mm:ss) Elapsed Time Program Time: 00:38:48 (hh:mm:ss) Elapsed Time