RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FeBEBw/RM_8665.FriJan120545362024 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: 1705067134 Database = /dev/shm/rModeler.FeBEBw/GCA_028858595.1_bGruAme1.pat - Sequences = 395 - Bases = 1200805165 - N50 = 125197326 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203747393-218300715 | [ 1 ] 189194071-203747392 | [ ] 174640750-189194071 | [ ] 160087428-174640749 | [ 1 ] 145534107-160087428 | [ ] 130980785-145534106 | [ ] 116427464-130980785 | [ 1 ] 101874142-116427463 | [ ] 87320821-101874142 | [ ] 72767499-87320820 | [ 2 ] 58214178-72767499 | [ 1 ] 43660856-58214177 | [ ] 29107535-43660856 | [ 4 ] 14554213-29107534 |* [ 8 ] 892-14554213 |************************************************** [ 377 ] Storage Throughput = excellent ( 1205.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40371428 bp ( 40037998 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:56 (hh:mm:ss) Elapsed Time Round Time: 00:28:58 (hh:mm:ss) Elapsed Time : 40 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 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1360 repeats masked totaling 537831 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10111322 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10038959 bp After Masking: 9475667 bp Masked: 5.61 % -- Input Database Coverage: 10111322 bp out of 1200805165 bp ( 0.84 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:17 (hh:mm:ss) Elapsed Time, 624 HSPs Collected Number of families returned by RECON: 269 Round Time: 00:07:11 (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 : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3753 repeats masked totaling 1495865 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30300139 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30039072 bp After Masking: 28355630 bp Masked: 5.60 % -- Input Database Coverage: 40411461 bp out of 1200805165 bp ( 3.37 % ) Sampling Time: 00:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:37:06 (hh:mm:ss) Elapsed Time, 5522 HSPs Collected Number of families returned by RECON: 1578 Round Time: 00:40:03 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14704 repeats masked totaling 5287448 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90390414 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 90029396 bp After Masking: 84390849 bp Masked: 6.26 % -- Input Database Coverage: 130801875 bp out of 1200805165 bp ( 10.89 % ) Sampling Time: 00:07:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 05:04:40 (hh:mm:ss) Elapsed Time, 32585 HSPs Collected Number of families returned by RECON: 8990 Round Time: 05:39:48 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55369 repeats masked totaling 18456481 bp(s). - TE Masking time 00:02:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271336081 bp Num Contigs Represented = 168 Non ambiguous bp: Initial: 270005995 bp After Masking: 250152085 bp Masked: 7.35 % -- Input Database Coverage: 402137956 bp out of 1200805165 bp ( 33.49 % ) Sampling Time: 00:33:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 47:13:15 (hh:mm:ss) Elapsed Time, 163394 HSPs Collected Number of families returned by RECON: 57426 Round Time: 48:38:44 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatScout/RECON discovery complete: 333 families found Classification Time: 00:29:03 (hh:mm:ss) Elapsed Time Program Time: 56:03:47 (hh:mm:ss) Elapsed Time