RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.lxGTGg/RM_1774232.MonDec21730002024 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: 1733189399 Database = /scratch/tmp/rModeler.lxGTGg/GCF_947461875.1_bHalAlb1.1 - Sequences = 189 - Bases = 1320315924 - N50 = 44572131 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 80014046-85729264 | [ 2 ] 74298828-80014045 | [ 1 ] 68583611-74298828 | [ 1 ] 62868393-68583610 | [ ] 57153176-62868393 | [ ] 51437958-57153175 | [ 1 ] 45722740-51437957 |* [ 4 ] 40007523-45722740 |* [ 6 ] 34292305-40007522 | [ 2 ] 28577088-34292305 |* [ 4 ] 22861870-28577087 |** [ 8 ] 17146652-22861869 | [ 1 ] 11431435-17146652 | [ ] 5716217-11431434 | [ 1 ] 1000-5716217 |************************************************** [ 158 ] Storage Throughput = excellent ( 1453.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019218 bp ( 40017218 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:24 (hh:mm:ss) Elapsed Time Round Time: 00:10:33 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1320 repeats masked totaling 552635 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008057 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10007457 bp After Masking: 8973316 bp Masked: 10.33 % -- Input Database Coverage: 10008057 bp out of 1320315924 bp ( 0.76 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 634 HSPs Collected Number of families returned by RECON: 287 Round Time: 00:03:57 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5537 repeats masked totaling 2275207 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011081 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30009681 bp After Masking: 26113258 bp Masked: 12.98 % -- Input Database Coverage: 40019138 bp out of 1320315924 bp ( 3.03 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:15:22 (hh:mm:ss) Elapsed Time, 8928 HSPs Collected Number of families returned by RECON: 1445 Round Time: 00:17:30 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17853 repeats masked totaling 7218741 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027843 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 90022243 bp After Masking: 78482116 bp Masked: 12.82 % -- Input Database Coverage: 130046981 bp out of 1320315924 bp ( 9.85 % ) Sampling Time: 00:05:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:33:27 (hh:mm:ss) Elapsed Time, 39054 HSPs Collected Number of families returned by RECON: 8521 Round Time: 01:40:10 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62919 repeats masked totaling 24357531 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037017 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270020617 bp After Masking: 232486072 bp Masked: 13.90 % -- Input Database Coverage: 400083998 bp out of 1320315924 bp ( 30.30 % ) Sampling Time: 00:11:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 11:45:57 (hh:mm:ss) Elapsed Time, 190123 HSPs Collected Number of families returned by RECON: 54099 Round Time: 12:19:34 (hh:mm:ss) Elapsed Time : 246 families discovered. RepeatScout/RECON discovery complete: 423 families found Classification Time: 00:17:46 (hh:mm:ss) Elapsed Time Program Time: 14:49:30 (hh:mm:ss) Elapsed Time