RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.VTDLKG/RM_2020888.WedNov131958472024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1731556726 Database = /scratch/tmp/rModeler.VTDLKG/GCF_036373705.1_fAmiCal2.hap1 - Sequences = 389 - Bases = 989103751 - N50 = 44214953 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 60087555-64379224 | [ 2 ] 55795886-60087554 | [ 1 ] 51504217-55795885 | [ 2 ] 47212548-51504216 | [ 2 ] 42920879-47212547 | [ 3 ] 38629210-42920878 | [ 1 ] 34337541-38629209 | [ 3 ] 30045872-34337540 | [ 2 ] 25754203-30045871 | [ 3 ] 21462534-25754202 | [ 4 ] 17170865-21462533 | [ ] 12879196-17170864 | [ ] 8587527-12879195 | [ ] 4295858-8587526 | [ ] 4190-4295858 |************************************************** [ 366 ] Storage Throughput = excellent ( 1457.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017721 bp ( 40016121 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:13 (hh:mm:ss) Elapsed Time Round Time: 00:14:14 (hh:mm:ss) Elapsed Time : 457 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6575 repeats masked totaling 2399348 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033395 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10032395 bp After Masking: 7113076 bp Masked: 29.10 % -- Input Database Coverage: 10033395 bp out of 989103751 bp ( 1.01 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 5508 HSPs Collected Number of families returned by RECON: 1103 Round Time: 00:03:33 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20153 repeats masked totaling 6825667 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024324 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30023724 bp After Masking: 21536926 bp Masked: 28.27 % -- Input Database Coverage: 40057719 bp out of 989103751 bp ( 4.05 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:13:32 (hh:mm:ss) Elapsed Time, 41015 HSPs Collected Number of families returned by RECON: 3532 Round Time: 00:17:02 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68221 repeats masked totaling 22292661 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013238 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 90011838 bp After Masking: 62988593 bp Masked: 30.02 % -- Input Database Coverage: 130070957 bp out of 989103751 bp ( 13.15 % ) Sampling Time: 00:06:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 01:14:02 (hh:mm:ss) Elapsed Time, 237893 HSPs Collected Number of families returned by RECON: 11307 Round Time: 01:23:58 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 245647 repeats masked totaling 77257651 bp(s). - TE Masking time 00:04:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015363 bp Num Contigs Represented = 222 Non ambiguous bp: Initial: 270011563 bp After Masking: 177742099 bp Masked: 34.17 % -- Input Database Coverage: 400086320 bp out of 989103751 bp ( 40.45 % ) Sampling Time: 00:22:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 09:49:35 (hh:mm:ss) Elapsed Time, 970506 HSPs Collected Number of families returned by RECON: 39732 Round Time: 10:35:10 (hh:mm:ss) Elapsed Time : 945 families discovered. RepeatScout/RECON discovery complete: 1855 families found Classification Time: 00:53:45 (hh:mm:ss) Elapsed Time Program Time: 13:27:42 (hh:mm:ss) Elapsed Time