RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.jPsLmA/RM_1458216.SatNov160530142024 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: 1731763814 Database = /scratch/tmp/rModeler.jPsLmA/GCA_019677235.1_HNU_Msal_1.0 - Sequences = 202 - Bases = 877669248 - N50 = 37225388 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52449540-56195885 | [ 1 ] 48703196-52449540 | [ ] 44956852-48703196 | [ 1 ] 41210508-44956852 | [ 2 ] 37464164-41210508 |* [ 5 ] 33717820-37464164 |** [ 10 ] 29971476-33717820 | [ 2 ] 26225131-29971475 | [ 2 ] 22478787-26225131 | [ ] 18732443-22478787 | [ ] 14986099-18732443 | [ ] 11239755-14986099 | [ ] 7493411-11239755 | [ ] 3747067-7493411 | [ ] 723-3747067 |************************************************** [ 179 ] Storage Throughput = excellent ( 1428.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016935 bp ( 40002993 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:32 (hh:mm:ss) Elapsed Time Round Time: 00:10:05 (hh:mm:ss) Elapsed Time : 962 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12826 repeats masked totaling 2163914 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040911 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10035911 bp After Masking: 7708802 bp Masked: 23.19 % -- Input Database Coverage: 10040911 bp out of 877669248 bp ( 1.14 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:13 (hh:mm:ss) Elapsed Time, 14518 HSPs Collected Number of families returned by RECON: 1861 Round Time: 00:04:08 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39312 repeats masked totaling 6446874 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015944 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30007002 bp After Masking: 22892323 bp Masked: 23.71 % -- Input Database Coverage: 40056855 bp out of 877669248 bp ( 4.56 % ) Sampling Time: 00:02:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:17:06 (hh:mm:ss) Elapsed Time, 62980 HSPs Collected Number of families returned by RECON: 6356 Round Time: 00:21:00 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132073 repeats masked totaling 21785736 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90052378 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90014878 bp After Masking: 66027238 bp Masked: 26.65 % -- Input Database Coverage: 130109233 bp out of 877669248 bp ( 14.82 % ) Sampling Time: 00:06:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:24:18 (hh:mm:ss) Elapsed Time, 368598 HSPs Collected Number of families returned by RECON: 19852 Round Time: 01:38:51 (hh:mm:ss) Elapsed Time : 655 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482113 repeats masked totaling 84803163 bp(s). - TE Masking time 00:04:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270123068 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 270011986 bp After Masking: 178819717 bp Masked: 33.77 % -- Input Database Coverage: 400232301 bp out of 877669248 bp ( 45.60 % ) Sampling Time: 00:26:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 09:29:47 (hh:mm:ss) Elapsed Time, 1042198 HSPs Collected Number of families returned by RECON: 63187 Round Time: 10:44:48 (hh:mm:ss) Elapsed Time : 1444 families discovered. RepeatScout/RECON discovery complete: 3249 families found Classification Time: 01:03:47 (hh:mm:ss) Elapsed Time Program Time: 14:02:39 (hh:mm:ss) Elapsed Time