RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.cD2syw/RM_405548.WedMay101029092023 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: 1683739747 Database = /dev/shm/rModeler.cD2syw/GCA_027574665.1_bRhyJub1.pri - Sequences = 148 - Bases = 1331454348 - N50 = 77456406 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 138725330-148633065 | [ 1 ] 128817596-138725330 | [ 1 ] 118909862-128817596 | [ 1 ] 109002127-118909861 | [ ] 99094393-109002127 | [ ] 89186659-99094393 | [ ] 79278925-89186659 | [ 1 ] 69371190-79278924 | [ 2 ] 59463456-69371190 | [ 1 ] 49555722-59463456 | [ ] 39647988-49555722 | [ 2 ] 29740253-39647987 | [ 2 ] 19832519-29740253 |** [ 7 ] 9924785-19832519 |**** [ 10 ] 17051-9924785 |************************************************** [ 120 ] Storage Throughput = excellent ( 1115.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017951 bp ( 40010403 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:37 (hh:mm:ss) Elapsed Time Round Time: 00:21:14 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1777 repeats masked totaling 660051 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024194 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10023194 bp After Masking: 8291205 bp Masked: 17.28 % -- Input Database Coverage: 10024194 bp out of 1331454348 bp ( 0.75 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:54 (hh:mm:ss) Elapsed Time, 302 HSPs Collected Number of families returned by RECON: 149 Round Time: 00:08:41 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6181 repeats masked totaling 2020477 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033766 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30027218 bp After Masking: 24696253 bp Masked: 17.75 % -- Input Database Coverage: 40057960 bp out of 1331454348 bp ( 3.01 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:37:17 (hh:mm:ss) Elapsed Time, 7354 HSPs Collected Number of families returned by RECON: 1024 Round Time: 00:42:31 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19447 repeats masked totaling 6262240 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90080093 bp Num Contigs Represented = 89 Non ambiguous bp: Initial: 90012358 bp After Masking: 74161636 bp Masked: 17.61 % -- Input Database Coverage: 130138053 bp out of 1331454348 bp ( 9.77 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 04:27:09 (hh:mm:ss) Elapsed Time, 194189 HSPs Collected Number of families returned by RECON: 6606 Round Time: 04:39:50 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63030 repeats masked totaling 20393966 bp(s). - TE Masking time 00:02:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270163877 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 270019644 bp After Masking: 218196843 bp Masked: 19.19 % -- Input Database Coverage: 400301930 bp out of 1331454348 bp ( 30.07 % ) Sampling Time: 00:37:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 28:49:10 (hh:mm:ss) Elapsed Time, 1804352 HSPs Collected Number of families returned by RECON: 41919 Round Time: 30:53:08 (hh:mm:ss) Elapsed Time : 208 families discovered. RepeatScout/RECON discovery complete: 322 families found Classification Time: 00:47:12 (hh:mm:ss) Elapsed Time Program Time: 37:32:36 (hh:mm:ss) Elapsed Time