RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Xaatrb/RM_3723241.MonMay150746562023 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: 1684162015 Database = /dev/shm/rModeler.Xaatrb/GCF_009829125.3_fPerMag1.2.pri - Sequences = 122 - Bases = 752605561 - N50 = 33436419 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34523101-36988977 |*** [ 6 ] 32057225-34523100 |**** [ 8 ] 29591349-32057224 |* [ 2 ] 27125473-29591348 |** [ 5 ] 24659597-27125472 | [ ] 22193721-24659596 | [ 1 ] 19727845-22193720 | [ ] 17261969-19727844 |* [ 2 ] 14796093-17261968 | [ ] 12330217-14796092 | [ ] 9864341-12330216 | [ ] 7398465-9864340 | [ ] 4932589-7398464 | [ ] 2466713-4932588 | [ ] 838-2466713 |************************************************** [ 98 ] Storage Throughput = excellent ( 1173.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40350869 bp ( 40007491 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:38 (hh:mm:ss) Elapsed Time Round Time: 00:21:27 (hh:mm:ss) Elapsed Time : 653 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22371 repeats masked totaling 3047006 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10143259 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10008100 bp After Masking: 6413298 bp Masked: 35.92 % -- Input Database Coverage: 10143259 bp out of 752605561 bp ( 1.35 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:07:17 (hh:mm:ss) Elapsed Time, 4559 HSPs Collected Number of families returned by RECON: 955 Round Time: 00:09:42 (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 : 00:00:29 (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... 66674 repeats masked totaling 9188879 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30247539 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30039320 bp After Masking: 19185185 bp Masked: 36.13 % -- Input Database Coverage: 40390798 bp out of 752605561 bp ( 5.37 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:34:08 (hh:mm:ss) Elapsed Time, 35245 HSPs Collected Number of families returned by RECON: 3632 Round Time: 00:39:59 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 210215 repeats masked totaling 29311650 bp(s). - TE Masking time 00:01:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90947473 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90011378 bp After Masking: 55707437 bp Masked: 38.11 % -- Input Database Coverage: 131338271 bp out of 752605561 bp ( 17.45 % ) Sampling Time: 00:14:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 03:19:06 (hh:mm:ss) Elapsed Time, 178385 HSPs Collected Number of families returned by RECON: 10894 Round Time: 03:40:19 (hh:mm:ss) Elapsed Time : 365 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 695876 repeats masked totaling 98961128 bp(s). - TE Masking time 00:09:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272405316 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270008828 bp After Masking: 155698412 bp Masked: 42.34 % -- Input Database Coverage: 403743587 bp out of 752605561 bp ( 53.65 % ) Sampling Time: 00:46:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23355195 Comparison Time: 23:13:05 (hh:mm:ss) Elapsed Time, 514682 HSPs Collected Number of families returned by RECON: 40402 Round Time: 24:46:10 (hh:mm:ss) Elapsed Time : 842 families discovered. RepeatScout/RECON discovery complete: 1971 families found Classification Time: 01:26:09 (hh:mm:ss) Elapsed Time Program Time: 31:03:46 (hh:mm:ss) Elapsed Time