RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IEOxc8/RM_21709.FriJan61804352023 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: 1673057074 Database = /dev/shm/rModeler.IEOxc8/GCA_947179515.1_mApoSyl1.1 - Sequences = 498 - Bases = 2889801511 - N50 = 132812118 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197646780-211764336 | [ 1 ] 183529224-197646779 | [ 1 ] 169411668-183529223 | [ 2 ] 155294113-169411668 | [ 1 ] 141176557-155294112 | [ 2 ] 127059001-141176556 | [ 1 ] 112941445-127059000 | [ 2 ] 98823890-112941445 | [ 4 ] 84706334-98823889 | [ 3 ] 70588778-84706333 | [ 2 ] 56471222-70588777 | [ 5 ] 42353667-56471222 | [ ] 28236111-42353666 | [ ] 14118555-28236110 | [ ] 1000-14118555 |************************************************** [ 474 ] Storage Throughput = excellent ( 1113.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013467 bp ( 40009867 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:02:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:04 (hh:mm:ss) Elapsed Time Round Time: 00:35:56 (hh:mm:ss) Elapsed Time : 260 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 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11155 repeats masked totaling 3166444 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009878 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10009078 bp After Masking: 5786853 bp Masked: 42.18 % -- Input Database Coverage: 10009878 bp out of 2889801511 bp ( 0.35 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:10 (hh:mm:ss) Elapsed Time, 6377 HSPs Collected Number of families returned by RECON: 679 Round Time: 00:08:16 (hh:mm:ss) Elapsed Time : 11 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 00:01:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36047 repeats masked totaling 9517881 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003509 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30000709 bp After Masking: 18289969 bp Masked: 39.03 % -- Input Database Coverage: 40013387 bp out of 2889801511 bp ( 1.38 % ) Sampling Time: 00:04:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:29:16 (hh:mm:ss) Elapsed Time, 19560 HSPs Collected Number of families returned by RECON: 2261 Round Time: 00:34:19 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118543 repeats masked totaling 30033860 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034267 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 90026067 bp After Masking: 53900611 bp Masked: 40.13 % -- Input Database Coverage: 130047654 bp out of 2889801511 bp ( 4.50 % ) Sampling Time: 00:12:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:04:10 (hh:mm:ss) Elapsed Time, 92141 HSPs Collected Number of families returned by RECON: 8070 Round Time: 03:21:22 (hh:mm:ss) Elapsed Time : 189 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 391314 repeats masked totaling 97103642 bp(s). - TE Masking time 00:06:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028183 bp Num Contigs Represented = 217 Non ambiguous bp: Initial: 270006712 bp After Masking: 152446331 bp Masked: 43.54 % -- Input Database Coverage: 400075837 bp out of 2889801511 bp ( 13.84 % ) Sampling Time: 00:41:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 22:17:53 (hh:mm:ss) Elapsed Time, 237280 HSPs Collected Number of families returned by RECON: 31567 Round Time: 23:30:42 (hh:mm:ss) Elapsed Time : 421 families discovered. RepeatScout/RECON discovery complete: 936 families found Classification Time: 00:49:44 (hh:mm:ss) Elapsed Time Program Time: 29:00:19 (hh:mm:ss) Elapsed Time