RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bTQbbL/RM_1279383.WedDec181107042024 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: 1734548824 Database = /dev/shm/rModeler.bTQbbL/GCA_039880925.1_mMolNig1.hap2 - Sequences = 282 - Bases = 2394902263 - N50 = 114774883 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 266679453-285727026 | [ 1 ] 247631881-266679453 | [ ] 228584309-247631881 | [ ] 209536737-228584309 | [ ] 190489165-209536737 | [ ] 171441593-190489165 | [ ] 152394021-171441593 | [ ] 133346449-152394021 | [ ] 114298877-133346449 |* [ 7 ] 95251305-114298877 | [ 5 ] 76203733-95251305 | [ 3 ] 57156161-76203733 | [ 4 ] 38108589-57156161 | [ 1 ] 19061017-38108589 | [ 2 ] 13445-19061017 |************************************************** [ 259 ] Storage Throughput = fair ( 485.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010730 bp ( 40010430 non ambiguous ) - Num Contigs Represented = 57 - Sequence extraction : 00:05:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:29:42 (hh:mm:ss) Elapsed Time Round Time: 01:02:13 (hh:mm:ss) Elapsed Time : 205 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11429 repeats masked totaling 3048344 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038588 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10038488 bp After Masking: 6832780 bp Masked: 31.93 % -- Input Database Coverage: 10038588 bp out of 2394902263 bp ( 0.42 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:11:24 (hh:mm:ss) Elapsed Time, 5727 HSPs Collected Number of families returned by RECON: 744 Round Time: 00:15:13 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38209 repeats masked totaling 9471427 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012068 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30011868 bp After Masking: 20090393 bp Masked: 33.06 % -- Input Database Coverage: 40050656 bp out of 2394902263 bp ( 1.67 % ) Sampling Time: 00:14:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 01:12:14 (hh:mm:ss) Elapsed Time, 27131 HSPs Collected Number of families returned by RECON: 2198 Round Time: 01:28:24 (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 : 00:09:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118208 repeats masked totaling 29857747 bp(s). - TE Masking time 00:03:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036135 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 90035735 bp After Masking: 58994139 bp Masked: 34.48 % -- Input Database Coverage: 130086791 bp out of 2394902263 bp ( 5.43 % ) Sampling Time: 00:22:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 09:32:46 (hh:mm:ss) Elapsed Time, 167748 HSPs Collected Number of families returned by RECON: 8020 Round Time: 10:06:49 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:28:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 389613 repeats masked totaling 97197548 bp(s). - TE Masking time 00:19:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011728 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 270010728 bp After Masking: 169252117 bp Masked: 37.32 % -- Input Database Coverage: 400098519 bp out of 2394902263 bp ( 16.71 % ) Sampling Time: 01:15:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 75:16:29 (hh:mm:ss) Elapsed Time, 1169568 HSPs Collected Number of families returned by RECON: 33069 Round Time: 77:13:40 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatScout/RECON discovery complete: 870 families found Classification Time: 01:31:37 (hh:mm:ss) Elapsed Time Program Time: 91:37:56 (hh:mm:ss) Elapsed Time