RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.keHTst/RM_2790598.MonMar101447402025 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: 1741643259 Database = /dev/shm/rModeler.keHTst/GCF_042767895.1_ASM4276789v1 - Sequences = 5444 - Bases = 1796890100 - N50 = 42894961 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52920224-56700184 | [ 4 ] 49140264-52920223 | [ 2 ] 45360304-49140263 | [ 7 ] 41580344-45360303 | [ 8 ] 37800384-41580343 | [ 3 ] 34020424-37800383 | [ 5 ] 30240464-34020423 | [ 6 ] 26460504-30240463 | [ 6 ] 22680544-26460503 | [ 2 ] 18900584-22680543 | [ ] 15120624-18900583 | [ ] 11340664-15120623 | [ ] 7560704-11340663 | [ ] 3780744-7560703 | [ 1 ] 785-3780744 |************************************************** [ 5400 ] Storage Throughput = excellent ( 1793.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40182284 bp ( 40022133 non ambiguous ) - Num Contigs Represented = 176 - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:32:38 (hh:mm:ss) Elapsed Time Round Time: 00:54:03 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3484 repeats masked totaling 471705 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10063890 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 10023857 bp After Masking: 5334268 bp Masked: 46.78 % -- Input Database Coverage: 10063890 bp out of 1796890100 bp ( 0.56 % ) Sampling Time: 00:12:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36046 Comparison Time: 00:06:43 (hh:mm:ss) Elapsed Time, 28219 HSPs Collected Number of families returned by RECON: 817 Round Time: 00:22:23 (hh:mm:ss) Elapsed Time : 16 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 00:43:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14542 repeats masked totaling 2980875 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30141988 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 30021870 bp After Masking: 14315489 bp Masked: 52.32 % -- Input Database Coverage: 40205878 bp out of 1796890100 bp ( 2.24 % ) Sampling Time: 00:44:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 339900 Comparison Time: 00:36:05 (hh:mm:ss) Elapsed Time, 37774 HSPs Collected Number of families returned by RECON: 2125 Round Time: 01:27:20 (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 : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:11:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46288 repeats masked totaling 9903352 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90389018 bp Num Contigs Represented = 353 Non ambiguous bp: Initial: 90025104 bp After Masking: 42183499 bp Masked: 53.14 % -- Input Database Coverage: 130594896 bp out of 1796890100 bp ( 7.27 % ) Sampling Time: 02:13:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3039345 Comparison Time: 03:20:28 (hh:mm:ss) Elapsed Time, 101852 HSPs Collected Number of families returned by RECON: 8008 Round Time: 05:41:02 (hh:mm:ss) Elapsed Time : 222 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 06:27:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 172489 repeats masked totaling 37227595 bp(s). - TE Masking time 00:08:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271097781 bp Num Contigs Represented = 911 Non ambiguous bp: Initial: 270010664 bp After Masking: 118865506 bp Masked: 55.98 % -- Input Database Coverage: 401692677 bp out of 1796890100 bp ( 22.35 % ) Sampling Time: 06:38:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26956153 Comparison Time: 21:59:25 (hh:mm:ss) Elapsed Time, 296434 HSPs Collected Number of families returned by RECON: 27118 Round Time: 29:08:49 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatScout/RECON discovery complete: 983 families found Classification Time: 00:22:31 (hh:mm:ss) Elapsed Time Program Time: 37:56:08 (hh:mm:ss) Elapsed Time