RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.P7fSPP/RM_47843.FriDec301413142022 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: 1672438393 Database = /dev/shm/rModeler.P7fSPP/GCF_905171765.1_aBufBuf1.1 - Sequences = 1306 - Bases = 5044744194 - N50 = 842558404 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 787141799-843366180 | [ 2 ] 730917418-787141798 | [ ] 674693038-730917418 | [ 1 ] 618468657-674693037 | [ 1 ] 562244277-618468657 | [ 1 ] 506019896-562244276 | [ ] 449795516-506019896 | [ ] 393571135-449795515 | [ 1 ] 337346755-393571135 | [ ] 281122374-337346754 | [ ] 224897994-281122374 | [ 3 ] 168673613-224897993 | [ ] 112449233-168673613 | [ 1 ] 56224852-112449232 | [ 1 ] 472-56224852 |************************************************** [ 1295 ] Storage Throughput = excellent ( 1428.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40065231 bp ( 40018196 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:12:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:59 (hh:mm:ss) Elapsed Time Round Time: 00:39:19 (hh:mm:ss) Elapsed Time : 1169 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20349 repeats masked totaling 5799869 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008468 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10007318 bp After Masking: 3276651 bp Masked: 67.26 % -- Input Database Coverage: 10008468 bp out of 5044744194 bp ( 0.20 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:10 (hh:mm:ss) Elapsed Time, 13367 HSPs Collected Number of families returned by RECON: 1325 Round Time: 00:10:57 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:10:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62828 repeats masked totaling 17650268 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30056683 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30010798 bp After Masking: 9631571 bp Masked: 67.91 % -- Input Database Coverage: 40065151 bp out of 5044744194 bp ( 0.79 % ) Sampling Time: 00:14:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:19:10 (hh:mm:ss) Elapsed Time, 51860 HSPs Collected Number of families returned by RECON: 4078 Round Time: 00:35:33 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:39:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 197474 repeats masked totaling 54828371 bp(s). - TE Masking time 00:03:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90253003 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90008804 bp After Masking: 27053081 bp Masked: 69.94 % -- Input Database Coverage: 130318154 bp out of 5044744194 bp ( 2.58 % ) Sampling Time: 00:56:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:54:25 (hh:mm:ss) Elapsed Time, 300328 HSPs Collected Number of families returned by RECON: 10283 Round Time: 03:11:20 (hh:mm:ss) Elapsed Time : 488 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:37:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 650304 repeats masked totaling 178334925 bp(s). - TE Masking time 00:15:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270733280 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270027408 bp After Masking: 65630616 bp Masked: 75.69 % -- Input Database Coverage: 401051434 bp out of 5044744194 bp ( 7.95 % ) Sampling Time: 02:20:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 11:35:10 (hh:mm:ss) Elapsed Time, 953495 HSPs Collected Number of families returned by RECON: 23755 Round Time: 14:56:59 (hh:mm:ss) Elapsed Time : 1283 families discovered. RepeatScout/RECON discovery complete: 3060 families found Classification Time: 02:27:32 (hh:mm:ss) Elapsed Time Program Time: 22:01:40 (hh:mm:ss) Elapsed Time