RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zaPZ8U/RM_362794.SatJan141258552023 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: 1673729935 Database = /dev/shm/rModeler.zaPZ8U/GCF_007399415.2_rGopEvg1_v1.p - Sequences = 383 - Bases = 2298564209 - N50 = 155918640 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 345646520-370335144 | [ 1 ] 320957897-345646520 | [ ] 296269273-320957896 | [ 1 ] 271580650-296269273 | [ ] 246892027-271580650 | [ ] 222203403-246892026 | [ 1 ] 197514780-222203403 | [ ] 172826156-197514779 | [ ] 148137533-172826156 | [ 1 ] 123448910-148137533 | [ 3 ] 98760286-123448909 | [ 2 ] 74071663-98760286 | [ 2 ] 49383039-74071662 | [ ] 24694416-49383039 | [ 6 ] 5793-24694416 |************************************************** [ 366 ] Storage Throughput = excellent ( 1631.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40608656 bp ( 40015722 non ambiguous ) - Num Contigs Represented = 55 - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:59 (hh:mm:ss) Elapsed Time Round Time: 00:23:02 (hh:mm:ss) Elapsed Time : 571 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13504 repeats masked totaling 2995976 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10280183 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10002651 bp After Masking: 6908504 bp Masked: 30.93 % -- Input Database Coverage: 10280183 bp out of 2298564209 bp ( 0.45 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:07:27 (hh:mm:ss) Elapsed Time, 13368 HSPs Collected Number of families returned by RECON: 1626 Round Time: 00:09:16 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43587 repeats masked totaling 10077659 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30328393 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30012991 bp After Masking: 19491807 bp Masked: 35.06 % -- Input Database Coverage: 40608576 bp out of 2298564209 bp ( 1.77 % ) Sampling Time: 00:04:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:26:18 (hh:mm:ss) Elapsed Time, 51473 HSPs Collected Number of families returned by RECON: 4629 Round Time: 00:31:55 (hh:mm:ss) Elapsed Time : 119 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 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145221 repeats masked totaling 33142560 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91294092 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90002471 bp After Masking: 55604311 bp Masked: 38.22 % -- Input Database Coverage: 131902668 bp out of 2298564209 bp ( 5.74 % ) Sampling Time: 00:09:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 02:00:43 (hh:mm:ss) Elapsed Time, 215044 HSPs Collected Number of families returned by RECON: 13738 Round Time: 02:17:18 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 505445 repeats masked totaling 113693329 bp(s). - TE Masking time 00:05:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273163651 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 270025631 bp After Masking: 152634573 bp Masked: 43.47 % -- Input Database Coverage: 405066319 bp out of 2298564209 bp ( 17.62 % ) Sampling Time: 00:38:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23492085 Comparison Time: 11:53:29 (hh:mm:ss) Elapsed Time, 629922 HSPs Collected Number of families returned by RECON: 43296 Round Time: 13:12:57 (hh:mm:ss) Elapsed Time : 1047 families discovered. RepeatScout/RECON discovery complete: 2194 families found Classification Time: 00:59:49 (hh:mm:ss) Elapsed Time Program Time: 17:34:17 (hh:mm:ss) Elapsed Time