RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EFUf8u/RM_7264.FriDec80553352023 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: 1702043613 Database = /dev/shm/rModeler.EFUf8u/GCA_950295315.1_mEriEur2.1 - Sequences = 1175 - Bases = 2720701264 - N50 = 127350028 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 196830474-210889723 | [ 2 ] 182771226-196830474 | [ 1 ] 168711978-182771226 | [ ] 154652730-168711978 | [ ] 140593482-154652730 | [ 1 ] 126534233-140593481 | [ 5 ] 112474985-126534233 | [ 2 ] 98415737-112474985 | [ 3 ] 84356489-98415737 | [ 2 ] 70297241-84356489 | [ 3 ] 56237992-70297240 | [ 2 ] 42178744-56237992 | [ 1 ] 28119496-42178744 | [ ] 14060248-28119496 | [ 2 ] 1000-14060248 |************************************************** [ 1151 ] Storage Throughput = excellent ( 1124.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015690 bp ( 40005290 non ambiguous ) - Num Contigs Represented = 75 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:53 (hh:mm:ss) Elapsed Time Round Time: 00:32:15 (hh:mm:ss) Elapsed Time : 265 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22386 repeats masked totaling 5109917 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022264 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10020464 bp After Masking: 4668093 bp Masked: 53.41 % -- Input Database Coverage: 10022264 bp out of 2720701264 bp ( 0.37 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:03 (hh:mm:ss) Elapsed Time, 3652 HSPs Collected Number of families returned by RECON: 406 Round Time: 00:06:57 (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 : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66081 repeats masked totaling 15043396 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033349 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30024749 bp After Masking: 14302693 bp Masked: 52.36 % -- Input Database Coverage: 40055613 bp out of 2720701264 bp ( 1.47 % ) Sampling Time: 00:04:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:31:37 (hh:mm:ss) Elapsed Time, 30537 HSPs Collected Number of families returned by RECON: 1416 Round Time: 00:43:41 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 204673 repeats masked totaling 45906550 bp(s). - TE Masking time 00:02:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90053821 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 90028221 bp After Masking: 41850905 bp Masked: 53.51 % -- Input Database Coverage: 130109434 bp out of 2720701264 bp ( 4.78 % ) Sampling Time: 00:15:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 02:36:22 (hh:mm:ss) Elapsed Time, 51128 HSPs Collected Number of families returned by RECON: 5447 Round Time: 02:54:07 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 663955 repeats masked totaling 143753884 bp(s). - TE Masking time 00:09:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270082589 bp Num Contigs Represented = 291 Non ambiguous bp: Initial: 270002719 bp After Masking: 119984287 bp Masked: 55.56 % -- Input Database Coverage: 400192023 bp out of 2720701264 bp ( 14.71 % ) Sampling Time: 00:45:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 19:08:25 (hh:mm:ss) Elapsed Time, 214872 HSPs Collected Number of families returned by RECON: 20708 Round Time: 20:07:42 (hh:mm:ss) Elapsed Time : 294 families discovered. RepeatScout/RECON discovery complete: 716 families found Classification Time: 00:31:43 (hh:mm:ss) Elapsed Time Program Time: 24:56:25 (hh:mm:ss) Elapsed Time