RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.oe4r8H/RM_2495226.TueDec31450342024 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: 1733266234 Database = /scratch/tmp/rModeler.oe4r8H/GCA_964276385.1_fGasAcu3.hap2.1 - Sequences = 170 - Bases = 457351142 - N50 = 22032426 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32503500-34825108 | [ 1 ] 30181893-32503500 | [ 1 ] 27860286-30181893 | [ 1 ] 25538679-27860286 | [ ] 23217072-25538679 | [ 2 ] 20895464-23217071 |* [ 5 ] 18573857-20895464 |** [ 6 ] 16252250-18573857 |* [ 4 ] 13930643-16252250 | [ ] 11609036-13930643 | [ ] 9287428-11609035 | [ ] 6965821-9287428 | [ ] 4644214-6965821 | [ ] 2322607-4644214 | [ ] 1000-2322607 |************************************************** [ 150 ] Storage Throughput = excellent ( 1551.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026018 bp ( 40018818 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:24 (hh:mm:ss) Elapsed Time Round Time: 00:09:47 (hh:mm:ss) Elapsed Time : 259 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2980 repeats masked totaling 811064 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007187 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10005387 bp After Masking: 8305671 bp Masked: 16.99 % -- Input Database Coverage: 10007187 bp out of 457351142 bp ( 2.19 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:40 (hh:mm:ss) Elapsed Time, 6893 HSPs Collected Number of families returned by RECON: 785 Round Time: 00:03:22 (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 : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9995 repeats masked totaling 2758377 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018818 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30013418 bp After Masking: 25012483 bp Masked: 16.66 % -- Input Database Coverage: 40026005 bp out of 457351142 bp ( 8.75 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:12:21 (hh:mm:ss) Elapsed Time, 41240 HSPs Collected Number of families returned by RECON: 3845 Round Time: 00:15:02 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34369 repeats masked totaling 8930968 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048213 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 90035813 bp After Masking: 74910701 bp Masked: 16.80 % -- Input Database Coverage: 130074218 bp out of 457351142 bp ( 28.44 % ) Sampling Time: 00:07:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 01:17:37 (hh:mm:ss) Elapsed Time, 189725 HSPs Collected Number of families returned by RECON: 15679 Round Time: 01:31:09 (hh:mm:ss) Elapsed Time : 279 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134910 repeats masked totaling 35461669 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060488 bp Num Contigs Represented = 145 Non ambiguous bp: Initial: 270025088 bp After Masking: 217276324 bp Masked: 19.53 % -- Input Database Coverage: 400134706 bp out of 457351142 bp ( 87.49 % ) Sampling Time: 00:17:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 09:39:00 (hh:mm:ss) Elapsed Time, 700454 HSPs Collected Number of families returned by RECON: 67991 Round Time: 10:35:09 (hh:mm:ss) Elapsed Time : 727 families discovered. RepeatScout/RECON discovery complete: 1315 families found Classification Time: 00:38:48 (hh:mm:ss) Elapsed Time Program Time: 13:13:17 (hh:mm:ss) Elapsed Time