RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RtrjHv/RM_29367.SatJul271336382024 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: 1722112597 Database = /dev/shm/rModeler.RtrjHv/GCF_020615455.1_ASM2061545v1 - Sequences = 7334 - Bases = 2753287365 - N50 = 52301279 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 93004450-99647553 | [ 1 ] 86361347-93004449 | [ ] 79718245-86361347 | [ ] 73075142-79718244 | [ 2 ] 66432040-73075142 | [ 2 ] 59788937-66432039 | [ 7 ] 53145834-59788936 | [ 8 ] 46502732-53145834 | [ 5 ] 39859629-46502731 | [ 6 ] 33216527-39859629 | [ 4 ] 26573424-33216526 | [ ] 19930321-26573423 | [ 2 ] 13287219-19930321 | [ ] 6644116-13287218 | [ 2 ] 1014-6644116 |************************************************** [ 7295 ] Storage Throughput = excellent ( 1029.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003209 bp ( 40001690 non ambiguous ) - Num Contigs Represented = 355 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:20 (hh:mm:ss) Elapsed Time Round Time: 00:32:08 (hh:mm:ss) Elapsed Time : 864 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14040 repeats masked totaling 4828458 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006406 bp Num Contigs Represented = 123 Non ambiguous bp: Initial: 10006196 bp After Masking: 3694384 bp Masked: 63.08 % -- Input Database Coverage: 10006406 bp out of 2753287365 bp ( 0.36 % ) Sampling Time: 00:04:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:15:46 (hh:mm:ss) Elapsed Time, 6046 HSPs Collected Number of families returned by RECON: 882 Round Time: 00:20:28 (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 : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43508 repeats masked totaling 14531878 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036795 bp Num Contigs Represented = 279 Non ambiguous bp: Initial: 30035486 bp After Masking: 11540362 bp Masked: 61.58 % -- Input Database Coverage: 40043201 bp out of 2753287365 bp ( 1.45 % ) Sampling Time: 00:12:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 313236 Comparison Time: 00:21:21 (hh:mm:ss) Elapsed Time, 33060 HSPs Collected Number of families returned by RECON: 3301 Round Time: 00:35:22 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134639 repeats masked totaling 43810738 bp(s). - TE Masking time 00:02:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009373 bp Num Contigs Represented = 665 Non ambiguous bp: Initial: 90005530 bp After Masking: 33999322 bp Masked: 62.23 % -- Input Database Coverage: 130052574 bp out of 2753287365 bp ( 4.72 % ) Sampling Time: 00:39:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2828631 Comparison Time: 02:40:27 (hh:mm:ss) Elapsed Time, 246155 HSPs Collected Number of families returned by RECON: 9641 Round Time: 03:28:45 (hh:mm:ss) Elapsed Time : 501 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:43:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 455882 repeats masked totaling 142576377 bp(s). - TE Masking time 00:12:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014735 bp Num Contigs Represented = 1714 Non ambiguous bp: Initial: 270001174 bp After Masking: 89319838 bp Masked: 66.92 % -- Input Database Coverage: 400067309 bp out of 2753287365 bp ( 14.53 % ) Sampling Time: 02:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25586281 Comparison Time: 12:28:18 (hh:mm:ss) Elapsed Time, 647537 HSPs Collected Number of families returned by RECON: 30378 Round Time: 15:15:49 (hh:mm:ss) Elapsed Time : 1005 families discovered. RepeatScout/RECON discovery complete: 2443 families found Classification Time: 01:58:07 (hh:mm:ss) Elapsed Time Program Time: 22:10:39 (hh:mm:ss) Elapsed Time