RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5o7Wlj/RM_3284072.ThuMar140610552024 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: 1710421854 Database = /dev/shm/rModeler.5o7Wlj/GCA_035084275.1_sHydCol1.hap2 - Sequences = 532 - Bases = 1003172678 - N50 = 111046537 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 145690701-156096171 | [ 1 ] 135285232-145690701 | [ 1 ] 124879763-135285232 | [ ] 114474294-124879763 | [ ] 104068825-114474294 | [ 1 ] 93663355-104068824 | [ ] 83257886-93663355 | [ 1 ] 72852417-83257886 | [ ] 62446948-72852417 | [ ] 52041479-62446948 | [ ] 41636009-52041478 | [ 1 ] 31230540-41636009 | [ ] 20825071-31230540 | [ 5 ] 10419602-20825071 |* [ 12 ] 14133-10419602 |************************************************** [ 510 ] Storage Throughput = excellent ( 1167.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40053256 bp ( 40036336 non ambiguous ) - Num Contigs Represented = 101 - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:43 (hh:mm:ss) Elapsed Time Round Time: 00:24:34 (hh:mm:ss) Elapsed Time : 348 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26678 repeats masked totaling 4101933 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021427 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10016592 bp After Masking: 5369540 bp Masked: 46.39 % -- Input Database Coverage: 10021427 bp out of 1003172678 bp ( 1.00 % ) Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:30 (hh:mm:ss) Elapsed Time, 10047 HSPs Collected Number of families returned by RECON: 551 Round Time: 00:09:00 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80285 repeats masked totaling 12223357 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031828 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 30019743 bp After Masking: 16326073 bp Masked: 45.62 % -- Input Database Coverage: 40053255 bp out of 1003172678 bp ( 3.99 % ) Sampling Time: 00:07:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:31:39 (hh:mm:ss) Elapsed Time, 14592 HSPs Collected Number of families returned by RECON: 2146 Round Time: 00:40:15 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 250760 repeats masked totaling 37731474 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90066780 bp Num Contigs Represented = 159 Non ambiguous bp: Initial: 90033866 bp After Masking: 48092824 bp Masked: 46.58 % -- Input Database Coverage: 130120035 bp out of 1003172678 bp ( 12.97 % ) Sampling Time: 00:22:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 02:48:31 (hh:mm:ss) Elapsed Time, 75440 HSPs Collected Number of families returned by RECON: 8040 Round Time: 03:15:34 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:56:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 795284 repeats masked totaling 119701931 bp(s). - TE Masking time 00:07:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270128489 bp Num Contigs Represented = 288 Non ambiguous bp: Initial: 270031374 bp After Masking: 137239914 bp Masked: 49.18 % -- Input Database Coverage: 400248524 bp out of 1003172678 bp ( 39.90 % ) Sampling Time: 01:13:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23191455 Comparison Time: 18:16:32 (hh:mm:ss) Elapsed Time, 317122 HSPs Collected Number of families returned by RECON: 32382 Round Time: 19:56:06 (hh:mm:ss) Elapsed Time : 562 families discovered. RepeatScout/RECON discovery complete: 1128 families found Classification Time: 00:42:10 (hh:mm:ss) Elapsed Time Program Time: 25:07:39 (hh:mm:ss) Elapsed Time