RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.XoDVeA/RM_2810772.SatNov160209112024 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: 1731751750 Database = /scratch/tmp/rModeler.XoDVeA/GCF_036417665.1_bPasDom1.hap1 - Sequences = 335 - Bases = 1310131054 - N50 = 84378497 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 150346880-161085800 | [ 1 ] 139607960-150346880 | [ ] 128869040-139607960 | [ ] 118130120-128869040 | [ 2 ] 107391200-118130120 | [ ] 96652280-107391200 | [ ] 85913360-96652280 | [ ] 75174440-85913360 | [ 3 ] 64435520-75174440 | [ 1 ] 53696600-64435520 | [ 2 ] 42957680-53696600 | [ 3 ] 32218760-42957680 | [ 1 ] 21479840-32218760 | [ 1 ] 10740920-21479840 |* [ 8 ] 2000-10740920 |************************************************** [ 313 ] Storage Throughput = excellent ( 1500.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021829 bp ( 40021229 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:33 (hh:mm:ss) Elapsed Time Round Time: 00:15:20 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3146 repeats masked totaling 1214926 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009184 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10008984 bp After Masking: 7630294 bp Masked: 23.77 % -- Input Database Coverage: 10009184 bp out of 1310131054 bp ( 0.76 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:36 (hh:mm:ss) Elapsed Time, 329443 HSPs Collected Number of families returned by RECON: 228 Round Time: 00:05:37 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9193 repeats masked totaling 3278543 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012565 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30012165 bp After Masking: 23331038 bp Masked: 22.26 % -- Input Database Coverage: 40021749 bp out of 1310131054 bp ( 3.05 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:23:16 (hh:mm:ss) Elapsed Time, 3255233 HSPs Collected Number of families returned by RECON: 1453 Round Time: 00:26:50 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38956 repeats masked totaling 11850314 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011405 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 90009805 bp After Masking: 69843089 bp Masked: 22.41 % -- Input Database Coverage: 130033154 bp out of 1310131054 bp ( 9.93 % ) Sampling Time: 00:07:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:29:43 (hh:mm:ss) Elapsed Time, 520954 HSPs Collected Number of families returned by RECON: 8706 Round Time: 01:39:26 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123272 repeats masked totaling 39080257 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036369 bp Num Contigs Represented = 169 Non ambiguous bp: Initial: 270028169 bp After Masking: 203270970 bp Masked: 24.72 % -- Input Database Coverage: 400069523 bp out of 1310131054 bp ( 30.54 % ) Sampling Time: 00:26:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 10:08:29 (hh:mm:ss) Elapsed Time, 4348021 HSPs Collected Number of families returned by RECON: 57287 Round Time: 11:01:35 (hh:mm:ss) Elapsed Time : 317 families discovered. RepeatScout/RECON discovery complete: 585 families found Classification Time: 00:27:00 (hh:mm:ss) Elapsed Time Program Time: 13:55:48 (hh:mm:ss) Elapsed Time