RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.aSzGY2/RM_865510.MonNov180221542024 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: 1731925314 Database = /scratch/tmp/rModeler.aSzGY2/GCF_963930625.1_mMunRee1.1 - Sequences = 267 - Bases = 2656168540 - N50 = 125491292 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 266773663-285828854 | [ 3 ] 247718473-266773663 | [ ] 228663283-247718473 | [ ] 209608092-228663282 | [ ] 190552902-209608092 | [ ] 171497712-190552902 | [ 1 ] 152442522-171497712 | [ ] 133387331-152442521 | [ 1 ] 114332141-133387331 | [ 2 ] 95276951-114332141 | [ 2 ] 76221761-95276951 | [ 4 ] 57166570-76221760 |* [ 7 ] 38111380-57166570 | [ 3 ] 19056190-38111380 | [ ] 1000-19056190 |************************************************** [ 244 ] Storage Throughput = excellent ( 1506.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010605 bp ( 40009605 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:09 (hh:mm:ss) Elapsed Time Round Time: 00:17:45 (hh:mm:ss) Elapsed Time : 245 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14118 repeats masked totaling 3538466 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002327 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10002327 bp After Masking: 6275055 bp Masked: 37.26 % -- Input Database Coverage: 10002327 bp out of 2656168540 bp ( 0.38 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:01 (hh:mm:ss) Elapsed Time, 5619 HSPs Collected Number of families returned by RECON: 645 Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44566 repeats masked totaling 10295409 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008198 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30007198 bp After Masking: 18992398 bp Masked: 36.71 % -- Input Database Coverage: 40010525 bp out of 2656168540 bp ( 1.51 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:13:16 (hh:mm:ss) Elapsed Time, 18216 HSPs Collected Number of families returned by RECON: 2198 Round Time: 00:16:32 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140913 repeats masked totaling 33111532 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010559 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 90005951 bp After Masking: 55081642 bp Masked: 38.80 % -- Input Database Coverage: 130021084 bp out of 2656168540 bp ( 4.90 % ) Sampling Time: 00:08:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:17:15 (hh:mm:ss) Elapsed Time, 66953 HSPs Collected Number of families returned by RECON: 7129 Round Time: 01:27:24 (hh:mm:ss) Elapsed Time : 160 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 454370 repeats masked totaling 106863636 bp(s). - TE Masking time 00:02:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270029421 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 270017221 bp After Masking: 158580262 bp Masked: 41.27 % -- Input Database Coverage: 400050505 bp out of 2656168540 bp ( 15.06 % ) Sampling Time: 00:25:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 08:36:27 (hh:mm:ss) Elapsed Time, 194573 HSPs Collected Number of families returned by RECON: 30823 Round Time: 09:11:26 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 840 families found Classification Time: 00:20:29 (hh:mm:ss) Elapsed Time Program Time: 11:37:57 (hh:mm:ss) Elapsed Time