RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.TjsK6j/RM_2141749.FriNov151701282024 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: 1731718888 Database = /scratch/tmp/rModeler.TjsK6j/GCF_036850765.1_mSacBil1_pri_phased_curated - Sequences = 256 - Bases = 2612309609 - N50 = 317915018 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 381195639-408423836 | [ 2 ] 353967442-381195638 | [ ] 326739245-353967441 | [ ] 299511049-326739245 | [ 2 ] 272282852-299511048 | [ ] 245054655-272282851 | [ 1 ] 217826458-245054654 | [ ] 190598262-217826458 | [ 1 ] 163370065-190598261 | [ ] 136141868-163370064 | [ 1 ] 108913671-136141867 | [ 1 ] 81685475-108913671 | [ 3 ] 54457278-81685474 | [ 2 ] 27229081-54457277 | [ ] 885-27229081 |************************************************** [ 243 ] Storage Throughput = excellent ( 1484.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40573293 bp ( 40017844 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:02:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:45 (hh:mm:ss) Elapsed Time Round Time: 00:17:47 (hh:mm:ss) Elapsed Time : 310 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12566 repeats masked totaling 3400904 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10240862 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10005549 bp After Masking: 6471565 bp Masked: 35.32 % -- Input Database Coverage: 10240862 bp out of 2612309609 bp ( 0.39 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 4881 HSPs Collected Number of families returned by RECON: 803 Round Time: 00:04:09 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39256 repeats masked totaling 11121781 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30332351 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30012215 bp After Masking: 18461787 bp Masked: 38.49 % -- Input Database Coverage: 40573213 bp out of 2612309609 bp ( 1.55 % ) Sampling Time: 00:02:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:12:18 (hh:mm:ss) Elapsed Time, 19737 HSPs Collected Number of families returned by RECON: 2126 Round Time: 00:15:39 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127353 repeats masked totaling 35353773 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90836280 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90014316 bp After Masking: 53537733 bp Masked: 40.52 % -- Input Database Coverage: 131409493 bp out of 2612309609 bp ( 5.03 % ) Sampling Time: 00:08:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 01:07:45 (hh:mm:ss) Elapsed Time, 75986 HSPs Collected Number of families returned by RECON: 7163 Round Time: 01:18:05 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415587 repeats masked totaling 113397478 bp(s). - TE Masking time 00:02:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273466847 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270008091 bp After Masking: 153140877 bp Masked: 43.28 % -- Input Database Coverage: 404876340 bp out of 2612309609 bp ( 15.50 % ) Sampling Time: 00:27:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23457825 Comparison Time: 07:28:24 (hh:mm:ss) Elapsed Time, 198545 HSPs Collected Number of families returned by RECON: 29401 Round Time: 08:04:34 (hh:mm:ss) Elapsed Time : 384 families discovered. RepeatScout/RECON discovery complete: 932 families found Classification Time: 00:18:58 (hh:mm:ss) Elapsed Time Program Time: 10:19:12 (hh:mm:ss) Elapsed Time