RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.c979gS/RM_2121946.MonSep81314462025 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: 1757362486 Database = /dev/shm/rModeler.c979gS/GCA_001023035.1_ASM102303v1 - Sequences = 187 - Bases = 43110459 - N50 = 1224341 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 3043859-3261259 | [ 1 ] 2826459-3043858 | [ ] 2609059-2826458 | [ ] 2391660-2609059 | [ 1 ] 2174260-2391659 | [ 1 ] 1956860-2174259 | [ ] 1739460-1956859 | [ 1 ] 1522061-1739460 |* [ 4 ] 1304661-1522060 | [ 2 ] 1087261-1304660 |* [ 4 ] 869861-1087260 |** [ 6 ] 652462-869861 |* [ 4 ] 435062-652461 |** [ 7 ] 217662-435061 |*** [ 10 ] 263-217662 |************************************************** [ 146 ] Storage Throughput = excellent ( 1657.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40196272 bp ( 40014976 non ambiguous ) - Num Contigs Represented = 181 - 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.. : 12 raw families identified - RepeatScout: Running filtering stage.. 12 families remaining - RepeatScout: 00:00:39 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 10 families... 00:00:05 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:00:50 (hh:mm:ss) Elapsed Time : 10 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... 335 repeats masked totaling 38911 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10059222 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 10008396 bp After Masking: 9960960 bp Masked: 0.47 % -- Input Database Coverage: 10059222 bp out of 43110459 bp ( 23.33 % ) Sampling Time: 00:00:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:03:46 (hh:mm:ss) Elapsed Time, 2262 HSPs Collected Number of families returned by RECON: 650 Round Time: 00:03:57 (hh:mm:ss) Elapsed Time : 1 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... 1268 repeats masked totaling 132831 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30137001 bp Num Contigs Represented = 156 Non ambiguous bp: Initial: 30006531 bp After Masking: 29854779 bp Masked: 0.51 % -- Input Database Coverage: 40196223 bp out of 43110459 bp ( 93.24 % ) Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 377146 Comparison Time: 00:15:49 (hh:mm:ss) Elapsed Time, 12152 HSPs Collected Number of families returned by RECON: 3483 Round Time: 00:16:26 (hh:mm:ss) Elapsed Time : 10 families discovered. - Increasing sample size to include end piece now = 93051237 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 93051237 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131 repeats masked totaling 15146 bp(s). - TE Masking time 00:00:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 2914065 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 2900065 bp After Masking: 2882022 bp Masked: 0.62 % -- Input Database Coverage: 43110288 bp out of 43110459 bp ( 100.00 % ) Sampling Time: 00:00:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3160 Comparison Time: 00:00:55 (hh:mm:ss) Elapsed Time, 84 HSPs Collected Number of families returned by RECON: 63 Round Time: 00:00:58 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 21 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.c979gS/RM_2121946.MonSep81314462025 # 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: 00:00:06 (hh:mm:ss) Elapsed Time Program Time: 00:22:17 (hh:mm:ss) Elapsed Time