RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.toBHI6/RM_3349315.MonMay81529092023 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: 1683584947 Database = /dev/shm/rModeler.toBHI6/GCA_026979555.1_bVidCha1_purged_dups_haplotype - Sequences = 1939 - Bases = 154870056 - N50 = 88229 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 616279-660102 | [ 2 ] 572457-616279 | [ ] 528635-572457 | [ ] 484812-528634 | [ ] 440990-484812 | [ 6 ] 397168-440990 | [ 7 ] 353345-397167 | [ 5 ] 309523-353345 | [ 4 ] 265701-309523 | [ 12 ] 221878-265700 | [ 19 ] 178056-221878 |* [ 38 ] 134234-178056 |***** [ 97 ] 90411-134233 |**************** [ 311 ] 46589-90411 |************************************************** [ 957 ] 2767-46589 |************************* [ 481 ] Storage Throughput = good ( 984.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006939 bp ( 40006939 non ambiguous ) - Num Contigs Represented = 957 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:01 (hh:mm:ss) Elapsed Time Round Time: 00:46:58 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5626 repeats masked totaling 3221782 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003401 bp Num Contigs Represented = 295 Non ambiguous bp: Initial: 10003401 bp After Masking: 5923336 bp Masked: 40.79 % -- Input Database Coverage: 10003401 bp out of 154870056 bp ( 6.46 % ) Sampling Time: 00:06:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 47586 Comparison Time: 00:32:07 (hh:mm:ss) Elapsed Time, 1731 HSPs Collected Number of families returned by RECON: 356 Round Time: 00:39:27 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18705 repeats masked totaling 10180578 bp(s). - TE Masking time 00:03:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003516 bp Num Contigs Represented = 758 Non ambiguous bp: Initial: 30003516 bp After Masking: 17267050 bp Masked: 42.45 % -- Input Database Coverage: 40006917 bp out of 154870056 bp ( 25.83 % ) Sampling Time: 00:11:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 433846 Comparison Time: 01:34:10 (hh:mm:ss) Elapsed Time, 15292 HSPs Collected Number of families returned by RECON: 1620 Round Time: 01:46:23 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57283 repeats masked totaling 31752218 bp(s). - TE Masking time 00:04:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040180 bp Num Contigs Represented = 1586 Non ambiguous bp: Initial: 90040180 bp After Masking: 50495397 bp Masked: 43.92 % -- Input Database Coverage: 130047097 bp out of 154870056 bp ( 83.97 % ) Sampling Time: 00:19:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3935415 Comparison Time: 03:38:23 (hh:mm:ss) Elapsed Time, 66917 HSPs Collected Number of families returned by RECON: 8872 Round Time: 04:17:26 (hh:mm:ss) Elapsed Time : 92 families discovered. - Increasing sample size to include end piece now = 294863139 RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16423 repeats masked totaling 9543364 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 24822768 bp Num Contigs Represented = 639 Non ambiguous bp: Initial: 24822768 bp After Masking: 13173066 bp Masked: 46.93 % -- Input Database Coverage: 154869865 bp out of 154870056 bp ( 100.00 % ) Sampling Time: 00:05:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:35:31 (hh:mm:ss) Elapsed Time, 2369 HSPs Collected Number of families returned by RECON: 981 Round Time: 00:41:05 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 352 families found Classification Time: 00:56:16 (hh:mm:ss) Elapsed Time Program Time: 09:07:35 (hh:mm:ss) Elapsed Time