RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.qh0JYG/RM_3819.MonDec21728192024 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: 1733189297 Database = /scratch/tmp/rModeler.qh0JYG/GCA_022682395.2_HLdesRot8B.1 - Sequences = 429 - Bases = 1969917660 - N50 = 167253561 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197086230-211163384 | [ 3 ] 183009077-197086230 | [ ] 168931924-183009077 | [ 1 ] 154854770-168931923 | [ 2 ] 140777617-154854770 | [ ] 126700464-140777617 | [ 1 ] 112623310-126700463 | [ 2 ] 98546157-112623310 | [ 3 ] 84469004-98546157 | [ 1 ] 70391850-84469003 | [ ] 56314697-70391850 | [ ] 42237544-56314697 | [ ] 28160390-42237543 | [ ] 14083237-28160390 | [ ] 6084-14083237 |************************************************** [ 416 ] Storage Throughput = fair ( 622.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004291 bp ( 40000051 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:03:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:05 (hh:mm:ss) Elapsed Time Round Time: 00:58:00 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7341 repeats masked totaling 2250053 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017706 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10016466 bp After Masking: 7714139 bp Masked: 22.99 % -- Input Database Coverage: 10017706 bp out of 1969917660 bp ( 0.51 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 12823 HSPs Collected Number of families returned by RECON: 935 Round Time: 00:07:04 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27466 repeats masked totaling 7798980 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026508 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30023508 bp After Masking: 21970170 bp Masked: 26.82 % -- Input Database Coverage: 40044214 bp out of 1969917660 bp ( 2.03 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:56 (hh:mm:ss) Elapsed Time, 33100 HSPs Collected Number of families returned by RECON: 2474 Round Time: 00:32:46 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90421 repeats masked totaling 24821235 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042168 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 90033728 bp After Masking: 64514211 bp Masked: 28.34 % -- Input Database Coverage: 130086382 bp out of 1969917660 bp ( 6.60 % ) Sampling Time: 00:11:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:16:50 (hh:mm:ss) Elapsed Time, 77352 HSPs Collected Number of families returned by RECON: 9349 Round Time: 03:34:04 (hh:mm:ss) Elapsed Time : 148 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 303715 repeats masked totaling 81938030 bp(s). - TE Masking time 00:05:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044801 bp Num Contigs Represented = 166 Non ambiguous bp: Initial: 270010361 bp After Masking: 185835851 bp Masked: 31.17 % -- Input Database Coverage: 400131183 bp out of 1969917660 bp ( 20.31 % ) Sampling Time: 00:36:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 25:57:01 (hh:mm:ss) Elapsed Time, 269625 HSPs Collected Number of families returned by RECON: 40442 Round Time: 27:18:54 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatScout/RECON discovery complete: 810 families found Classification Time: 00:34:47 (hh:mm:ss) Elapsed Time Program Time: 33:05:35 (hh:mm:ss) Elapsed Time