RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.I6Ak9N/RM_3868264.MonSep82029002025 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: 1757388539 Database = /dev/shm/rModeler.I6Ak9N/GCA_003316995.2_ASM331699v2 - Sequences = 258 - Bases = 42294396 - N50 = 4234806 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 5793188-6206916 | [ 1 ] 5379460-5793187 | [ ] 4965733-5379460 | [ ] 4552005-4965732 | [ 2 ] 4138278-4552005 | [ 2 ] 3724550-4138277 | [ 1 ] 3310822-3724549 | [ ] 2897095-3310822 | [ 2 ] 2483367-2897094 | [ 1 ] 2069640-2483367 | [ ] 1655912-2069639 | [ 1 ] 1242184-1655911 | [ 1 ] 828457-1242184 | [ ] 414729-828456 | [ ] 1002-414729 |************************************************* [ 247 ] Storage Throughput = excellent ( 1717.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40090948 bp ( 40019548 non ambiguous ) - Num Contigs Represented = 243 - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 42 raw families identified - RepeatScout: Running filtering stage.. 27 families remaining - RepeatScout: 00:00:44 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 27 families... 00:01:44 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 0 contained, found in 00:00:02 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:02 (hh:mm:ss) Elapsed Time Round Time: 00:02:35 (hh:mm:ss) Elapsed Time : 27 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 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 629 repeats masked totaling 135331 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10054703 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 10038403 bp After Masking: 9895420 bp Masked: 1.42 % -- Input Database Coverage: 10054703 bp out of 42294396 bp ( 23.77 % ) Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 45451 Comparison Time: 00:04:15 (hh:mm:ss) Elapsed Time, 1515 HSPs Collected Number of families returned by RECON: 643 Round Time: 00:05:00 (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 : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1928 repeats masked totaling 490904 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30083193 bp Num Contigs Represented = 193 Non ambiguous bp: Initial: 30028093 bp After Masking: 29505651 bp Masked: 1.74 % -- Input Database Coverage: 40137896 bp out of 42294396 bp ( 94.90 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 419986 Comparison Time: 00:17:39 (hh:mm:ss) Elapsed Time, 11288 HSPs Collected Number of families returned by RECON: 3192 Round Time: 00:29:40 (hh:mm:ss) Elapsed Time : 7 families discovered. - Increasing sample size to include end piece now = 92239693 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 92239693 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... 160 repeats masked totaling 30218 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 2156207 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 2152507 bp After Masking: 2120855 bp Masked: 1.47 % -- Input Database Coverage: 42294103 bp out of 42294396 bp ( 100.00 % ) Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2211 Comparison Time: 00:00:45 (hh:mm:ss) Elapsed Time, 42 HSPs Collected Number of families returned by RECON: 37 Round Time: 00:01:01 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 36 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.I6Ak9N/RM_3868264.MonSep82029002025 # 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: 00:00:10 (hh:mm:ss) Elapsed Time Program Time: 00:38:26 (hh:mm:ss) Elapsed Time