RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.9OLm03/RM_86602.MonSep82040442025 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: 1757389243 Database = /dev/shm/rModeler.9OLm03/GCA_003610855.1_ASM361085v1 - Sequences = 10900 - Bases = 41983253 - N50 = 7259 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 47372-50729 | [ 1 ] 44016-47372 | [ 1 ] 40660-44016 | [ 2 ] 37303-40659 | [ 4 ] 33947-37303 | [ 5 ] 30591-33947 | [ 7 ] 27235-30591 | [ 14 ] 23878-27234 | [ 36 ] 20522-23878 | [ 61 ] 17166-20522 | [ 97 ] 13810-17166 |* [ 205 ] 10453-13809 |*** [ 470 ] 7097-10453 |***** [ 867 ] 3741-7097 |************* [ 1894 ] 385-3741 |************************************************** [ 7236 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = excellent ( 1639.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40276884 bp ( 40000180 non ambiguous ) - Num Contigs Represented = 10429 - 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.. : 779 raw families identified - RepeatScout: Running filtering stage.. 777 families remaining - RepeatScout: 00:01:24 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 741 families... 00:01:29 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 109 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:02:59 (hh:mm:ss) Elapsed Time : 632 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 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9540 repeats masked totaling 2775426 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10074090 bp Num Contigs Represented = 2615 Non ambiguous bp: Initial: 10002804 bp After Masking: 7221372 bp Masked: 27.81 % -- Input Database Coverage: 10074090 bp out of 41983253 bp ( 24.00 % ) Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3420420 Comparison Time: 00:11:46 (hh:mm:ss) Elapsed Time, 13735 HSPs Collected Number of families returned by RECON: 2223 Round Time: 00:12:19 (hh:mm:ss) Elapsed Time : 19 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 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30300 repeats masked totaling 8886558 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30205551 bp Num Contigs Represented = 7818 Non ambiguous bp: Initial: 30000127 bp After Masking: 21095557 bp Masked: 29.68 % -- Input Database Coverage: 40279641 bp out of 41983253 bp ( 95.94 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 30572290 Comparison Time: 00:40:21 (hh:mm:ss) Elapsed Time, 104435 HSPs Collected Number of families returned by RECON: 5888 Round Time: 00:42:47 (hh:mm:ss) Elapsed Time : 266 families discovered. - Increasing sample size to include end piece now = 91909163 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 91909163 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2209 repeats masked totaling 669814 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 1703481 bp Num Contigs Represented = 469 Non ambiguous bp: Initial: 1691448 bp After Masking: 1022001 bp Masked: 39.58 % -- Input Database Coverage: 41983122 bp out of 41983253 bp ( 100.00 % ) Sampling Time: 00:00:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 109746 Comparison Time: 00:01:57 (hh:mm:ss) Elapsed Time, 110 HSPs Collected Number of families returned by RECON: 95 Round Time: 00:02:02 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 917 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.9OLm03/RM_86602.MonSep82040442025 # 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: 00:01:17 (hh:mm:ss) Elapsed Time Program Time: 01:01:24 (hh:mm:ss) Elapsed Time