RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.btu2qj/RM_104414.SatJan70150262023 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: 1673085026 Database = /dev/shm/rModeler.btu2qj/GCF_910594005.1_mCerEla1.1 - Sequences = 144 - Bases = 2886603524 - N50 = 85849967 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 167957302-179953079 | [ 1 ] 155961525-167957301 | [ ] 143965748-155961524 | [ ] 131969971-143965747 | [ 2 ] 119974194-131969970 | [ 1 ] 107978417-119974193 | [ 2 ] 95982640-107978416 |* [ 3 ] 83986864-95982640 |* [ 3 ] 71991087-83986863 |** [ 5 ] 59995310-71991086 |*** [ 7 ] 47999533-59995309 |**** [ 9 ] 36003756-47999532 | [ 1 ] 24007979-36003755 | [ ] 12012202-24007978 | [ ] 16426-12012202 |************************************************* [ 110 ] Storage Throughput = excellent ( 1174.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018312 bp ( 40018312 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:01:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:09 (hh:mm:ss) Elapsed Time Round Time: 00:31:33 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11634 repeats masked totaling 2628793 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000857 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10000857 bp After Masking: 7045019 bp Masked: 29.56 % -- Input Database Coverage: 10000857 bp out of 2886603524 bp ( 0.35 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:08:37 (hh:mm:ss) Elapsed Time, 127845 HSPs Collected Number of families returned by RECON: 601 Round Time: 00:11:20 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37979 repeats masked totaling 8705182 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017448 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30017448 bp After Masking: 20597945 bp Masked: 31.38 % -- Input Database Coverage: 40018305 bp out of 2886603524 bp ( 1.39 % ) Sampling Time: 00:06:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:43:42 (hh:mm:ss) Elapsed Time, 989310 HSPs Collected Number of families returned by RECON: 2026 Round Time: 00:51:33 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121394 repeats masked totaling 27345602 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016508 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90015808 bp After Masking: 60879607 bp Masked: 32.37 % -- Input Database Coverage: 130034813 bp out of 2886603524 bp ( 4.50 % ) Sampling Time: 00:15:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 05:09:59 (hh:mm:ss) Elapsed Time, 7843705 HSPs Collected Number of families returned by RECON: 7690 Round Time: 05:33:08 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 403456 repeats masked totaling 89936692 bp(s). - TE Masking time 00:05:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270005696 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270005296 bp After Masking: 173910236 bp Masked: 35.59 % -- Input Database Coverage: 400040509 bp out of 2886603524 bp ( 13.86 % ) Sampling Time: 00:52:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 43:31:57 (hh:mm:ss) Elapsed Time, 81817264 HSPs Collected Number of families returned by RECON: 29652 Round Time: 46:00:09 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatScout/RECON discovery complete: 766 families found Classification Time: 00:49:42 (hh:mm:ss) Elapsed Time Program Time: 53:57:25 (hh:mm:ss) Elapsed Time