RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.UCcHCZ/RM_1163036.TueNov121153332024 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: 1731441211 Database = /scratch/tmp/rModeler.UCcHCZ/GCA_963971535.1_fNotCoa1.1 - Sequences = 5983 - Bases = 3427809033 - N50 = 182226839 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 301738038-323290686 | [ 1 ] 280185391-301738038 | [ ] 258632744-280185391 | [ ] 237080097-258632744 | [ ] 215527450-237080097 | [ 1 ] 193974803-215527450 | [ 3 ] 172422156-193974803 | [ 2 ] 150869508-172422155 | [ 2 ] 129316861-150869508 | [ 3 ] 107764214-129316861 | [ 5 ] 86211567-107764214 | [ 2 ] 64658920-86211567 | [ 1 ] 43106273-64658920 | [ ] 21553626-43106273 | [ ] 979-21553626 |************************************************** [ 5963 ] Storage Throughput = excellent ( 1564.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40067556 bp ( 40032423 non ambiguous ) - Num Contigs Represented = 121 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:28 (hh:mm:ss) Elapsed Time Round Time: 00:17:57 (hh:mm:ss) Elapsed Time : 1593 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20383 repeats masked totaling 5556253 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032003 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10024603 bp After Masking: 3066372 bp Masked: 69.41 % -- Input Database Coverage: 10032003 bp out of 3427809033 bp ( 0.29 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:02:48 (hh:mm:ss) Elapsed Time, 5818 HSPs Collected Number of families returned by RECON: 1489 Round Time: 00:05:22 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60130 repeats masked totaling 16942886 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035473 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 30007740 bp After Masking: 8742882 bp Masked: 70.86 % -- Input Database Coverage: 40067476 bp out of 3427809033 bp ( 1.17 % ) Sampling Time: 00:05:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:09:53 (hh:mm:ss) Elapsed Time, 46291 HSPs Collected Number of families returned by RECON: 4624 Round Time: 00:15:52 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 186479 repeats masked totaling 50176657 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90093793 bp Num Contigs Represented = 279 Non ambiguous bp: Initial: 90017988 bp After Masking: 26947948 bp Masked: 70.06 % -- Input Database Coverage: 130161269 bp out of 3427809033 bp ( 3.80 % ) Sampling Time: 00:18:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2731953 Comparison Time: 00:47:06 (hh:mm:ss) Elapsed Time, 404808 HSPs Collected Number of families returned by RECON: 11097 Round Time: 01:11:52 (hh:mm:ss) Elapsed Time : 726 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 639533 repeats masked totaling 170095746 bp(s). - TE Masking time 00:07:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270268196 bp Num Contigs Represented = 744 Non ambiguous bp: Initial: 270034211 bp After Masking: 62519540 bp Masked: 76.85 % -- Input Database Coverage: 400429465 bp out of 3427809033 bp ( 11.68 % ) Sampling Time: 00:55:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24805446 Comparison Time: 04:22:30 (hh:mm:ss) Elapsed Time, 1167363 HSPs Collected Number of families returned by RECON: 25959 Round Time: 05:42:25 (hh:mm:ss) Elapsed Time : 1805 families discovered. RepeatScout/RECON discovery complete: 4212 families found Classification Time: 01:24:27 (hh:mm:ss) Elapsed Time Program Time: 08:57:55 (hh:mm:ss) Elapsed Time