RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AAJbvp/RM_10960.WedNov290507542023 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: 1701263273 Database = /dev/shm/rModeler.AAJbvp/GCA_028564815.1_mEubGla1.hap2 - Sequences = 779 - Bases = 2832194838 - N50 = 133752502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 224782628-240837649 | [ 1 ] 208727607-224782627 | [ ] 192672587-208727607 | [ 2 ] 176617566-192672586 | [ 1 ] 160562545-176617565 | [ ] 144507525-160562545 | [ 2 ] 128452504-144507524 | [ 3 ] 112397483-128452503 | [ 3 ] 96342463-112397483 | [ 1 ] 80287442-96342462 | [ 5 ] 64232421-80287441 | [ 1 ] 48177401-64232421 | [ 2 ] 32122380-48177400 | [ ] 16067359-32122379 | [ ] 12339-16067359 |************************************************** [ 758 ] Storage Throughput = excellent ( 1138.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020525 bp ( 40019712 non ambiguous ) - Num Contigs Represented = 74 - Sequence extraction : 00:02:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:13 (hh:mm:ss) Elapsed Time Round Time: 00:44:30 (hh:mm:ss) Elapsed Time : 200 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 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8498 repeats masked totaling 2820318 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011623 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10011223 bp After Masking: 6855260 bp Masked: 31.52 % -- Input Database Coverage: 10011623 bp out of 2832194838 bp ( 0.35 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:05 (hh:mm:ss) Elapsed Time, 52942 HSPs Collected Number of families returned by RECON: 915 Round Time: 00:09:46 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30512 repeats masked totaling 10115139 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008822 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30008409 bp After Masking: 18982554 bp Masked: 36.74 % -- Input Database Coverage: 40020445 bp out of 2832194838 bp ( 1.41 % ) Sampling Time: 00:04:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:27:54 (hh:mm:ss) Elapsed Time, 46131 HSPs Collected Number of families returned by RECON: 2243 Round Time: 00:34:09 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101133 repeats masked totaling 33915681 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90153423 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 90031147 bp After Masking: 53681080 bp Masked: 40.37 % -- Input Database Coverage: 130173868 bp out of 2832194838 bp ( 4.60 % ) Sampling Time: 00:12:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:55:20 (hh:mm:ss) Elapsed Time, 464226 HSPs Collected Number of families returned by RECON: 7811 Round Time: 03:14:53 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 335267 repeats masked totaling 114539670 bp(s). - TE Masking time 00:06:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270620030 bp Num Contigs Represented = 280 Non ambiguous bp: Initial: 270019982 bp After Masking: 146914868 bp Masked: 45.59 % -- Input Database Coverage: 400793898 bp out of 2832194838 bp ( 14.15 % ) Sampling Time: 00:43:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 20:56:13 (hh:mm:ss) Elapsed Time, 399552 HSPs Collected Number of families returned by RECON: 29269 Round Time: 22:05:47 (hh:mm:ss) Elapsed Time : 330 families discovered. RepeatScout/RECON discovery complete: 769 families found Classification Time: 00:31:15 (hh:mm:ss) Elapsed Time Program Time: 27:20:20 (hh:mm:ss) Elapsed Time