RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.U7I2l9/RM_28387.MonMay151109472023 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: 1684174187 Database = /dev/shm/rModeler.U7I2l9/GCF_026979565.1_bVidCha1_merged_haplotype - Sequences = 177 - Bases = 1080440577 - N50 = 73120142 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 143328491-153566144 | [ 1 ] 133090838-143328490 | [ ] 122853186-133090838 | [ ] 112615533-122853185 | [ 2 ] 102377880-112615532 | [ ] 92140228-102377880 | [ ] 81902575-92140227 | [ ] 71664922-81902574 | [ 3 ] 61427270-71664922 | [ 1 ] 51189617-61427269 | [ ] 40951964-51189616 | [ ] 30714312-40951964 | [ 3 ] 20476659-30714311 |* [ 4 ] 10239006-20476658 |** [ 8 ] 1354-10239006 |************************************************** [ 155 ] Storage Throughput = excellent ( 1125.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036902 bp ( 40032602 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:07 (hh:mm:ss) Elapsed Time Round Time: 00:26:55 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2430 repeats masked totaling 585990 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008349 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10006949 bp After Masking: 9221447 bp Masked: 7.85 % -- Input Database Coverage: 10008349 bp out of 1080440577 bp ( 0.93 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:58 (hh:mm:ss) Elapsed Time, 485 HSPs Collected Number of families returned by RECON: 255 Round Time: 00:09:02 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7116 repeats masked totaling 1824751 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028549 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30025649 bp After Masking: 27650297 bp Masked: 7.91 % -- Input Database Coverage: 40036898 bp out of 1080440577 bp ( 3.71 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:43:49 (hh:mm:ss) Elapsed Time, 9215 HSPs Collected Number of families returned by RECON: 1848 Round Time: 00:47:03 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22808 repeats masked totaling 5769684 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015501 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 90000813 bp After Masking: 82172076 bp Masked: 8.70 % -- Input Database Coverage: 130052399 bp out of 1080440577 bp ( 12.04 % ) Sampling Time: 00:09:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 05:20:35 (hh:mm:ss) Elapsed Time, 75856 HSPs Collected Number of families returned by RECON: 11574 Round Time: 05:36:03 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 81064 repeats masked totaling 22773757 bp(s). - TE Masking time 00:04:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056137 bp Num Contigs Represented = 100 Non ambiguous bp: Initial: 270016856 bp After Masking: 241257788 bp Masked: 10.65 % -- Input Database Coverage: 400108536 bp out of 1080440577 bp ( 37.03 % ) Sampling Time: 00:30:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 43:15:59 (hh:mm:ss) Elapsed Time, 262849 HSPs Collected Number of families returned by RECON: 74197 Round Time: 45:07:34 (hh:mm:ss) Elapsed Time : 269 families discovered. RepeatScout/RECON discovery complete: 493 families found Classification Time: 00:33:19 (hh:mm:ss) Elapsed Time Program Time: 52:39:56 (hh:mm:ss) Elapsed Time