RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.A5rMo8/RM_19831.FriJan271114312023 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: 1674846870 Database = /dev/shm/rModeler.A5rMo8/GCF_947179515.1_mApoSyl1.1 - Sequences = 497 - Bases = 2889785202 - 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 |************************************************* [ 473 ] Storage Throughput = excellent ( 1080.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012412 bp ( 40008395 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:22 (hh:mm:ss) Elapsed Time Round Time: 00:35:47 (hh:mm:ss) Elapsed Time : 259 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11708 repeats masked totaling 3105918 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004345 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10002528 bp After Masking: 6331081 bp Masked: 36.71 % -- Input Database Coverage: 10004345 bp out of 2889785202 bp ( 0.35 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:44 (hh:mm:ss) Elapsed Time, 7410 HSPs Collected Number of families returned by RECON: 720 Round Time: 00:08:39 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38590 repeats masked totaling 9551837 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007987 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30005787 bp After Masking: 17653464 bp Masked: 41.17 % -- Input Database Coverage: 40012332 bp out of 2889785202 bp ( 1.38 % ) Sampling Time: 00:04:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:29:18 (hh:mm:ss) Elapsed Time, 18654 HSPs Collected Number of families returned by RECON: 2009 Round Time: 00:35:02 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118657 repeats masked totaling 30532492 bp(s). - TE Masking time 00:01:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044143 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 90037743 bp After Masking: 53051009 bp Masked: 41.08 % -- Input Database Coverage: 130056475 bp out of 2889785202 bp ( 4.50 % ) Sampling Time: 00:14:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:03:14 (hh:mm:ss) Elapsed Time, 103245 HSPs Collected Number of families returned by RECON: 8082 Round Time: 03:21:56 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 414431 repeats masked totaling 99214364 bp(s). - TE Masking time 00:07:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043705 bp Num Contigs Represented = 227 Non ambiguous bp: Initial: 270021905 bp After Masking: 150035163 bp Masked: 44.44 % -- Input Database Coverage: 400100180 bp out of 2889785202 bp ( 13.85 % ) Sampling Time: 00:41:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 21:53:07 (hh:mm:ss) Elapsed Time, 266899 HSPs Collected Number of families returned by RECON: 29161 Round Time: 23:29:56 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatScout/RECON discovery complete: 940 families found Classification Time: 00:58:13 (hh:mm:ss) Elapsed Time Program Time: 29:09:33 (hh:mm:ss) Elapsed Time