RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2R66wl/RM_11495.SatMay130922032023 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: 1683994922 Database = /dev/shm/rModeler.2R66wl/GCA_900634775.2_fGouWil2.2 - Sequences = 442 - Bases = 937169869 - N50 = 40234402 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 67622631-72451976 | [ 1 ] 62793286-67622630 | [ ] 57963941-62793285 | [ ] 53134596-57963940 | [ ] 48305251-53134595 | [ ] 43475906-48305250 | [ 4 ] 38646561-43475905 | [ 6 ] 33817217-38646561 | [ 5 ] 28987872-33817216 | [ 2 ] 24158527-28987871 | [ 4 ] 19329182-24158526 | [ ] 14499837-19329181 | [ ] 9670492-14499836 | [ 1 ] 4841147-9670491 | [ ] 11803-4841147 |************************************************* [ 419 ] Storage Throughput = excellent ( 1052.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40763543 bp ( 40002968 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:17 (hh:mm:ss) Elapsed Time Round Time: 00:34:10 (hh:mm:ss) Elapsed Time : 1265 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21767 repeats masked totaling 3743880 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10176809 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10020120 bp After Masking: 5887904 bp Masked: 41.24 % -- Input Database Coverage: 10176809 bp out of 937169869 bp ( 1.09 % ) Sampling Time: 00:01:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:08:06 (hh:mm:ss) Elapsed Time, 31890 HSPs Collected Number of families returned by RECON: 1576 Round Time: 00:13:10 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67616 repeats masked totaling 11481383 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30626583 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30022697 bp After Masking: 17398225 bp Masked: 42.05 % -- Input Database Coverage: 40803392 bp out of 937169869 bp ( 4.35 % ) Sampling Time: 00:04:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:34:09 (hh:mm:ss) Elapsed Time, 60537 HSPs Collected Number of families returned by RECON: 4907 Round Time: 00:41:01 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 213838 repeats masked totaling 35708026 bp(s). - TE Masking time 00:04:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91215711 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 90024521 bp After Masking: 51064240 bp Masked: 43.28 % -- Input Database Coverage: 132019103 bp out of 937169869 bp ( 14.09 % ) Sampling Time: 00:13:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2648451 Comparison Time: 03:39:51 (hh:mm:ss) Elapsed Time, 309345 HSPs Collected Number of families returned by RECON: 13904 Round Time: 04:08:43 (hh:mm:ss) Elapsed Time : 616 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 716605 repeats masked totaling 122485630 bp(s). - TE Masking time 00:24:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273893460 bp Num Contigs Represented = 244 Non ambiguous bp: Initial: 270010956 bp After Masking: 137616594 bp Masked: 49.03 % -- Input Database Coverage: 405912563 bp out of 937169869 bp ( 43.31 % ) Sampling Time: 00:52:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23836060 Comparison Time: 25:01:13 (hh:mm:ss) Elapsed Time, 854757 HSPs Collected Number of families returned by RECON: 41496 Round Time: 27:12:02 (hh:mm:ss) Elapsed Time : 1436 families discovered. RepeatScout/RECON discovery complete: 3461 families found Classification Time: 02:29:23 (hh:mm:ss) Elapsed Time Program Time: 35:18:29 (hh:mm:ss) Elapsed Time