RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tM4wYY/RM_379644.ThuJan120513462023 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: 1673529225 Database = /dev/shm/rModeler.tM4wYY/GCA_020800305.1_bPorHoc1.mat.Z.cur - Sequences = 174 - Bases = 1270294353 - N50 = 127874553 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 209173644-224114340 | [ 1 ] 194232949-209173644 | [ ] 179292254-194232949 | [ ] 164351559-179292254 | [ 1 ] 149410864-164351559 | [ ] 134470168-149410863 | [ ] 119529473-134470168 | [ 1 ] 104588778-119529473 | [ ] 89648083-104588778 | [ 1 ] 74707388-89648083 | [ ] 59766692-74707387 | [ 1 ] 44825997-59766692 | [ 1 ] 29885302-44825997 |* [ 4 ] 14944607-29885302 |** [ 9 ] 3912-14944607 |************************************************** [ 155 ] Storage Throughput = excellent ( 1162.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40137577 bp ( 40012278 non ambiguous ) - Num Contigs Represented = 63 - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:22 (hh:mm:ss) Elapsed Time Round Time: 00:17:57 (hh:mm:ss) Elapsed Time : 85 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2916 repeats masked totaling 1047202 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10059711 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10016062 bp After Masking: 8602742 bp Masked: 14.11 % -- Input Database Coverage: 10059711 bp out of 1270294353 bp ( 0.79 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:10:33 (hh:mm:ss) Elapsed Time, 1693 HSPs Collected Number of families returned by RECON: 181 Round Time: 00:12:33 (hh:mm:ss) Elapsed Time : 2 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 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9595 repeats masked totaling 3445042 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30117866 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30036216 bp After Masking: 25129991 bp Masked: 16.33 % -- Input Database Coverage: 40177577 bp out of 1270294353 bp ( 3.16 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:57:15 (hh:mm:ss) Elapsed Time, 4203 HSPs Collected Number of families returned by RECON: 1251 Round Time: 01:00:17 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29341 repeats masked totaling 10387028 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90395725 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90025893 bp After Masking: 75678693 bp Masked: 15.94 % -- Input Database Coverage: 130573302 bp out of 1270294353 bp ( 10.28 % ) Sampling Time: 00:13:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:22:37 (hh:mm:ss) Elapsed Time, 38538 HSPs Collected Number of families returned by RECON: 8479 Round Time: 02:37:27 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100348 repeats masked totaling 33758018 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271183593 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270024958 bp After Masking: 223437518 bp Masked: 17.25 % -- Input Database Coverage: 401756895 bp out of 1270294353 bp ( 31.63 % ) Sampling Time: 00:48:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 17:25:06 (hh:mm:ss) Elapsed Time, 169320 HSPs Collected Number of families returned by RECON: 55328 Round Time: 18:40:27 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatScout/RECON discovery complete: 372 families found Classification Time: 00:23:46 (hh:mm:ss) Elapsed Time Program Time: 23:12:27 (hh:mm:ss) Elapsed Time