RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rUv3Pp/RM_22281.SatJun291608352024 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: 1719702514 Database = /dev/shm/rModeler.rUv3Pp/GCA_022577435.1_fEmbJac1.0.p - Sequences = 230 - Bases = 634685148 - N50 = 17417607 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 25008050-26793196 |* [ 4 ] 23222904-25008049 | [ 1 ] 21437758-23222903 | [ 3 ] 19652613-21437758 | [ 3 ] 17867467-19652612 | [ 2 ] 16082321-17867466 | [ 1 ] 14297175-16082320 | [ 2 ] 12512030-14297175 | [ 2 ] 10726884-12512029 |* [ 5 ] 8941738-10726883 | [ ] 7156592-8941737 | [ 2 ] 5371447-7156592 |** [ 7 ] 3586301-5371446 |* [ 5 ] 1801155-3586300 |****** [ 22 ] 16010-1801155 |************************************************** [ 171 ] Storage Throughput = good ( 966.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008012 bp ( 40006412 non ambiguous ) - Num Contigs Represented = 125 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:54 (hh:mm:ss) Elapsed Time Round Time: 00:31:17 (hh:mm:ss) Elapsed Time : 244 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4313 repeats masked totaling 798419 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025606 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 10025206 bp After Masking: 8136644 bp Masked: 18.84 % -- Input Database Coverage: 10025606 bp out of 634685148 bp ( 1.58 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 5875 HSPs Collected Number of families returned by RECON: 1019 Round Time: 00:09:52 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15936 repeats masked totaling 2860185 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022448 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 30021248 bp After Masking: 25284790 bp Masked: 15.78 % -- Input Database Coverage: 40048054 bp out of 634685148 bp ( 6.31 % ) Sampling Time: 00:05:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:41:58 (hh:mm:ss) Elapsed Time, 46092 HSPs Collected Number of families returned by RECON: 4312 Round Time: 00:48:43 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58897 repeats masked totaling 10351753 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005847 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 90002147 bp After Masking: 73089694 bp Masked: 18.79 % -- Input Database Coverage: 130053901 bp out of 634685148 bp ( 20.49 % ) Sampling Time: 00:22:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 05:07:15 (hh:mm:ss) Elapsed Time, 155526 HSPs Collected Number of families returned by RECON: 16102 Round Time: 05:39:46 (hh:mm:ss) Elapsed Time : 293 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 223246 repeats masked totaling 39559081 bp(s). - TE Masking time 00:06:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041367 bp Num Contigs Represented = 203 Non ambiguous bp: Initial: 270032066 bp After Masking: 209399814 bp Masked: 22.45 % -- Input Database Coverage: 400095268 bp out of 634685148 bp ( 63.04 % ) Sampling Time: 01:12:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 40:57:32 (hh:mm:ss) Elapsed Time, 492357 HSPs Collected Number of families returned by RECON: 69726 Round Time: 44:01:07 (hh:mm:ss) Elapsed Time : 777 families discovered. RepeatScout/RECON discovery complete: 1421 families found Classification Time: 01:02:20 (hh:mm:ss) Elapsed Time Program Time: 52:13:05 (hh:mm:ss) Elapsed Time