RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.7JOyv1/RM_2402286.SunNov170733342024 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: 1731857614 Database = /scratch/tmp/rModeler.7JOyv1/GCF_036417845.1_bAptMan1.hap1 - Sequences = 408 - Bases = 1504396159 - N50 = 88548715 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 208065238-222926480 | [ 1 ] 193203997-208065238 | [ ] 178342756-193203997 | [ ] 163481515-178342756 | [ 1 ] 148620274-163481515 | [ ] 133759033-148620274 | [ 1 ] 118897792-133759033 | [ ] 104036550-118897791 | [ ] 89175309-104036550 | [ 1 ] 74314068-89175309 | [ 2 ] 59452827-74314068 | [ ] 44591586-59452827 | [ 2 ] 29730345-44591586 | [ 3 ] 14869104-29730345 |* [ 13 ] 7863-14869104 |************************************************** [ 384 ] Storage Throughput = excellent ( 1461.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035456 bp ( 40034456 non ambiguous ) - Num Contigs Represented = 93 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:37 (hh:mm:ss) Elapsed Time Round Time: 00:13:05 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2548 repeats masked totaling 1159802 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038940 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10038740 bp After Masking: 8265017 bp Masked: 17.67 % -- Input Database Coverage: 10038940 bp out of 1504396159 bp ( 0.67 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 1804 HSPs Collected Number of families returned by RECON: 337 Round Time: 00:04:07 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4808 repeats masked totaling 3041944 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036436 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30035636 bp After Masking: 25457903 bp Masked: 15.24 % -- Input Database Coverage: 40075376 bp out of 1504396159 bp ( 2.66 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:15:00 (hh:mm:ss) Elapsed Time, 13507 HSPs Collected Number of families returned by RECON: 1695 Round Time: 00:19:58 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23127 repeats masked totaling 10673369 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003661 bp Num Contigs Represented = 145 Non ambiguous bp: Initial: 90001261 bp After Masking: 75584983 bp Masked: 16.02 % -- Input Database Coverage: 130079037 bp out of 1504396159 bp ( 8.65 % ) Sampling Time: 00:06:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:26:36 (hh:mm:ss) Elapsed Time, 75138 HSPs Collected Number of families returned by RECON: 7910 Round Time: 01:47:12 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 91375 repeats masked totaling 43373664 bp(s). - TE Masking time 00:02:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008506 bp Num Contigs Represented = 218 Non ambiguous bp: Initial: 270001706 bp After Masking: 214563624 bp Masked: 20.53 % -- Input Database Coverage: 400087543 bp out of 1504396159 bp ( 26.59 % ) Sampling Time: 00:21:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 11:00:21 (hh:mm:ss) Elapsed Time, 366953 HSPs Collected Number of families returned by RECON: 46006 Round Time: 11:40:31 (hh:mm:ss) Elapsed Time : 334 families discovered. RepeatScout/RECON discovery complete: 558 families found Classification Time: 00:36:10 (hh:mm:ss) Elapsed Time Program Time: 14:41:03 (hh:mm:ss) Elapsed Time