RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4Wwr8N/RM_4088214.MonDec42228072023 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: 1701757687 Database = /dev/shm/rModeler.4Wwr8N/GCF_012275295.1_bMelUnd1.mat.Z - Sequences = 864 - Bases = 1171617451 - N50 = 112750338 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 144733677-155071706 | [ 1 ] 134395648-144733677 | [ ] 124057619-134395648 | [ ] 113719590-124057619 | [ 2 ] 103381561-113719590 | [ 2 ] 93043532-103381561 | [ ] 82705503-93043532 | [ 2 ] 72367474-82705503 | [ 1 ] 62029445-72367474 | [ ] 51691416-62029445 | [ 1 ] 41353387-51691416 | [ 1 ] 31015358-41353387 | [ 1 ] 20677329-31015358 | [ 2 ] 10339300-20677329 | [ 1 ] 1271-10339300 |************************************************** [ 850 ] Storage Throughput = excellent ( 1357.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40196395 bp ( 40036883 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:22 (hh:mm:ss) Elapsed Time Round Time: 00:22:15 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2772 repeats masked totaling 931099 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10077730 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10037107 bp After Masking: 8880346 bp Masked: 11.52 % -- Input Database Coverage: 10077730 bp out of 1171617451 bp ( 0.86 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:23 (hh:mm:ss) Elapsed Time, 404 HSPs Collected Number of families returned by RECON: 233 Round Time: 00:07:40 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10240 repeats masked totaling 3270265 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30158602 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30039713 bp After Masking: 26345684 bp Masked: 12.30 % -- Input Database Coverage: 40236332 bp out of 1171617451 bp ( 3.43 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:31:46 (hh:mm:ss) Elapsed Time, 4409 HSPs Collected Number of families returned by RECON: 1291 Round Time: 00:35:18 (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 : 00:04:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29156 repeats masked totaling 9164517 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90124508 bp Num Contigs Represented = 160 Non ambiguous bp: Initial: 90000082 bp After Masking: 79123124 bp Masked: 12.09 % -- Input Database Coverage: 130360840 bp out of 1171617451 bp ( 11.13 % ) Sampling Time: 00:11:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2625486 Comparison Time: 03:40:30 (hh:mm:ss) Elapsed Time, 28849 HSPs Collected Number of families returned by RECON: 8827 Round Time: 03:53:56 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 96484 repeats masked totaling 30009251 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270617100 bp Num Contigs Represented = 366 Non ambiguous bp: Initial: 270027430 bp After Masking: 234420726 bp Masked: 13.19 % -- Input Database Coverage: 400977940 bp out of 1171617451 bp ( 34.22 % ) Sampling Time: 00:36:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23656881 Comparison Time: 31:42:36 (hh:mm:ss) Elapsed Time, 236711 HSPs Collected Number of families returned by RECON: 60678 Round Time: 32:59:34 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatScout/RECON discovery complete: 332 families found Classification Time: 00:31:51 (hh:mm:ss) Elapsed Time Program Time: 38:30:34 (hh:mm:ss) Elapsed Time