RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.iXaj6i/RM_1720772.FriAug151201502025 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: 1755284509 Database = /data/tmp/rModeler.iXaj6i/GCA_001579985.1_ASM157998v1 - Sequences = 14960 - Bases = 182155491 - N50 = 17218 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 264903-283682 | [ 1 ] 246124-264902 | [ ] 227345-246123 | [ 1 ] 208566-227344 | [ ] 189788-208566 | [ 2 ] 171009-189787 | [ ] 152230-171008 | [ 2 ] 133451-152229 | [ 5 ] 114672-133450 | [ 10 ] 95894-114672 | [ 12 ] 77115-95893 | [ 32 ] 58336-77114 | [ 80 ] 39557-58335 |* [ 301 ] 20778-39556 |****** [ 1694 ] 2000-20778 |************************************************** [ 12820 ] Storage Throughput = good ( 994.08 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027332 bp ( 40020812 non ambiguous ) - Num Contigs Represented = 3356 - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:21 (hh:mm:ss) Elapsed Time Round Time: 00:31:05 (hh:mm:ss) Elapsed Time : 693 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 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10929 repeats masked totaling 1798475 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031118 bp Num Contigs Represented = 822 Non ambiguous bp: Initial: 10028970 bp After Masking: 7597526 bp Masked: 24.24 % -- Input Database Coverage: 10031118 bp out of 182155491 bp ( 5.51 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 339076 Comparison Time: 00:07:52 (hh:mm:ss) Elapsed Time, 3031 HSPs Collected Number of families returned by RECON: 1084 Round Time: 00:10:02 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33419 repeats masked totaling 5390896 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015954 bp Num Contigs Represented = 2546 Non ambiguous bp: Initial: 30011582 bp After Masking: 22802058 bp Masked: 24.02 % -- Input Database Coverage: 40047072 bp out of 182155491 bp ( 21.99 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3283203 Comparison Time: 00:33:53 (hh:mm:ss) Elapsed Time, 28549 HSPs Collected Number of families returned by RECON: 5205 Round Time: 00:41:56 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104535 repeats masked totaling 16138854 bp(s). - TE Masking time 00:03:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022063 bp Num Contigs Represented = 7572 Non ambiguous bp: Initial: 90002449 bp After Masking: 68389873 bp Masked: 24.01 % -- Input Database Coverage: 130069135 bp out of 182155491 bp ( 71.41 % ) Sampling Time: 00:10:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 29633451 Comparison Time: 03:00:42 (hh:mm:ss) Elapsed Time, 238511 HSPs Collected Number of families returned by RECON: 19294 Round Time: 03:42:52 (hh:mm:ss) Elapsed Time : 185 families discovered. - Increasing sample size to include end piece now = 322108419 RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66305 repeats masked totaling 10870061 bp(s). - TE Masking time 00:03:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 52086181 bp Num Contigs Represented = 4336 Non ambiguous bp: Initial: 52075990 bp After Masking: 38166977 bp Masked: 26.71 % -- Input Database Coverage: 182155316 bp out of 182155491 bp ( 100.00 % ) Sampling Time: 00:06:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 9616305 Comparison Time: 01:28:23 (hh:mm:ss) Elapsed Time, 51979 HSPs Collected Number of families returned by RECON: 9778 Round Time: 01:43:11 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatScout/RECON discovery complete: 935 families found Classification Time: 00:44:20 (hh:mm:ss) Elapsed Time Program Time: 07:33:26 (hh:mm:ss) Elapsed Time