RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IYbJbl/RM_90677.TueJan101332012023 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: 1673386320 Database = /dev/shm/rModeler.IYbJbl/GCA_009819605.1_bSteHir1.pri - Sequences = 123 - Bases = 1229972541 - N50 = 132030966 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 205472198-220148669 | [ 1 ] 190795727-205472197 | [ ] 176119256-190795726 | [ ] 161442786-176119256 | [ 1 ] 146766315-161442785 | [ ] 132089844-146766314 | [ ] 117413373-132089843 | [ 1 ] 102736903-117413373 | [ ] 88060432-102736902 | [ ] 73383961-88060431 |* [ 3 ] 58707490-73383960 | [ 2 ] 44031020-58707490 |* [ 3 ] 29354549-44031019 | [ 2 ] 14678078-29354548 | [ 1 ] 1608-14678078 |************************************************* [ 109 ] Storage Throughput = excellent ( 1212.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40210080 bp ( 40019508 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:24 (hh:mm:ss) Elapsed Time Round Time: 00:21:05 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2040 repeats masked totaling 735253 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043376 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10003276 bp After Masking: 9153995 bp Masked: 8.49 % -- Input Database Coverage: 10043376 bp out of 1229972541 bp ( 0.82 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:37 (hh:mm:ss) Elapsed Time, 497 HSPs Collected Number of families returned by RECON: 217 Round Time: 00:07:39 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6182 repeats masked totaling 2192872 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30166624 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30016152 bp After Masking: 27651820 bp Masked: 7.88 % -- Input Database Coverage: 40210000 bp out of 1229972541 bp ( 3.27 % ) Sampling Time: 00:02:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:35:58 (hh:mm:ss) Elapsed Time, 4872 HSPs Collected Number of families returned by RECON: 1422 Round Time: 00:39:20 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19295 repeats masked totaling 6715016 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90565847 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90008728 bp After Masking: 82793737 bp Masked: 8.02 % -- Input Database Coverage: 130775847 bp out of 1229972541 bp ( 10.63 % ) Sampling Time: 00:09:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 04:31:15 (hh:mm:ss) Elapsed Time, 32281 HSPs Collected Number of families returned by RECON: 8447 Round Time: 04:43:50 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68016 repeats masked totaling 22602342 bp(s). - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272592118 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 270025447 bp After Masking: 245989052 bp Masked: 8.90 % -- Input Database Coverage: 403367965 bp out of 1229972541 bp ( 32.79 % ) Sampling Time: 00:32:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 34:52:03 (hh:mm:ss) Elapsed Time, 164632 HSPs Collected Number of families returned by RECON: 52871 Round Time: 36:05:25 (hh:mm:ss) Elapsed Time : 221 families discovered. RepeatScout/RECON discovery complete: 361 families found Classification Time: 00:20:38 (hh:mm:ss) Elapsed Time Program Time: 42:17:57 (hh:mm:ss) Elapsed Time