RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Qpq2Ds/RM_2079574.WedFeb111936312026 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: 1770867391 Database = /dev/shm/rModeler.Qpq2Ds/GCA_012932265.1_ASM1293226v1 - Sequences = 14421 - Bases = 56351116 - N50 = 6114 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 89704-96097 | [ 1 ] 83311-89704 | [ ] 76918-83311 | [ 1 ] 70525-76918 | [ 1 ] 64132-70525 | [ 3 ] 57739-64132 | [ 3 ] 51346-57739 | [ 9 ] 44953-51346 | [ 8 ] 38560-44953 | [ 8 ] 32167-38560 | [ 35 ] 25774-32167 | [ 59 ] 19381-25774 | [ 119 ] 12988-19381 |* [ 373 ] 6595-12988 |***** [ 1469 ] 202-6595 |************************************************** [ 12332 ] 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 ( 1683.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009802 bp ( 40004683 non ambiguous ) - Num Contigs Represented = 10290 - 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.. : 407 raw families identified - RepeatScout: Running filtering stage.. 406 families remaining - RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 395 families... 00:00:39 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 77 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:01:46 (hh:mm:ss) Elapsed Time : 318 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 00:00:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4169 repeats masked totaling 1262163 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003622 bp Num Contigs Represented = 2518 Non ambiguous bp: Initial: 9999943 bp After Masking: 8726398 bp Masked: 12.74 % -- Input Database Coverage: 10003622 bp out of 56351116 bp ( 17.75 % ) Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3168903 Comparison Time: 00:09:34 (hh:mm:ss) Elapsed Time, 8061 HSPs Collected Number of families returned by RECON: 2041 Round Time: 00:09:56 (hh:mm:ss) Elapsed Time : 2 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 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13686 repeats masked totaling 4195254 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006103 bp Num Contigs Represented = 7776 Non ambiguous bp: Initial: 30004663 bp After Masking: 25775362 bp Masked: 14.10 % -- Input Database Coverage: 40009725 bp out of 56351116 bp ( 71.00 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 30307005 Comparison Time: 00:34:22 (hh:mm:ss) Elapsed Time, 78543 HSPs Collected Number of families returned by RECON: 7627 Round Time: 00:36:02 (hh:mm:ss) Elapsed Time : 92 families discovered. - Increasing sample size to include end piece now = 106347494 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 106347494 bp - Sequence extraction : 00:00:01 (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... 8716 repeats masked totaling 2877072 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 16341195 bp Num Contigs Represented = 4147 Non ambiguous bp: Initial: 16332610 bp After Masking: 13441039 bp Masked: 17.70 % -- Input Database Coverage: 56350920 bp out of 56351116 bp ( 100.00 % ) Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 8596731 Comparison Time: 00:16:43 (hh:mm:ss) Elapsed Time, 15055 HSPs Collected Number of families returned by RECON: 3508 Round Time: 00:17:17 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatScout/RECON discovery complete: 416 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Qpq2Ds/RM_2079574.WedFeb111936312026 # 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: 00:00:40 (hh:mm:ss) Elapsed Time Program Time: 01:05:41 (hh:mm:ss) Elapsed Time