RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DsAx5K/RM_23524.SunJul211027552024 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: 1721582874 Database = /dev/shm/rModeler.DsAx5K/GCF_016920845.1_GAculeatus_UGA_version5 - Sequences = 2937 - Bases = 471894361 - N50 = 20553084 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31902479-34181212 | [ 1 ] 29623747-31902479 | [ 1 ] 27345014-29623746 | [ 1 ] 25066282-27345014 | [ ] 22787550-25066282 | [ 1 ] 20508817-22787549 | [ 5 ] 18230085-20508817 | [ 4 ] 15951352-18230084 | [ 6 ] 13672620-15951352 | [ 3 ] 11393888-13672620 | [ ] 9115155-11393887 | [ ] 6836423-9115155 | [ ] 4557690-6836422 | [ ] 2278958-4557690 | [ ] 226-2278958 |************************************************** [ 2915 ] Storage Throughput = excellent ( 1126.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40280239 bp ( 40008914 non ambiguous ) - Num Contigs Represented = 288 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:02 (hh:mm:ss) Elapsed Time Round Time: 00:23:38 (hh:mm:ss) Elapsed Time : 306 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3829 repeats masked totaling 955490 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10096706 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 10035899 bp After Masking: 8859099 bp Masked: 11.73 % -- Input Database Coverage: 10096706 bp out of 471894361 bp ( 2.14 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 48516 Comparison Time: 00:12:58 (hh:mm:ss) Elapsed Time, 4886 HSPs Collected Number of families returned by RECON: 945 Round Time: 00:14:40 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11669 repeats masked totaling 2811133 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30223485 bp Num Contigs Represented = 218 Non ambiguous bp: Initial: 30012967 bp After Masking: 26649246 bp Masked: 11.21 % -- Input Database Coverage: 40320191 bp out of 471894361 bp ( 8.54 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 422740 Comparison Time: 00:53:59 (hh:mm:ss) Elapsed Time, 22047 HSPs Collected Number of families returned by RECON: 3810 Round Time: 00:57:51 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37102 repeats masked totaling 8626074 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90656802 bp Num Contigs Represented = 573 Non ambiguous bp: Initial: 90021913 bp After Masking: 79482411 bp Masked: 11.71 % -- Input Database Coverage: 130976993 bp out of 471894361 bp ( 27.76 % ) Sampling Time: 00:05:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3716901 Comparison Time: 05:40:27 (hh:mm:ss) Elapsed Time, 168305 HSPs Collected Number of families returned by RECON: 16605 Round Time: 06:09:05 (hh:mm:ss) Elapsed Time : 293 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 147709 repeats masked totaling 34575624 bp(s). - TE Masking time 00:08:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272060228 bp Num Contigs Represented = 1674 Non ambiguous bp: Initial: 270023773 bp After Masking: 230117405 bp Masked: 14.78 % -- Input Database Coverage: 403037221 bp out of 471894361 bp ( 85.41 % ) Sampling Time: 00:21:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33566721 Comparison Time: 54:21:42 (hh:mm:ss) Elapsed Time, 674906 HSPs Collected Number of families returned by RECON: 70749 Round Time: 57:15:42 (hh:mm:ss) Elapsed Time : 834 families discovered. RepeatScout/RECON discovery complete: 1481 families found Classification Time: 01:40:03 (hh:mm:ss) Elapsed Time Program Time: 66:40:59 (hh:mm:ss) Elapsed Time