RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qyGdSo/RM_23200.SatNov252138332023 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: 1700977112 Database = /dev/shm/rModeler.qyGdSo/GCA_012275265.1_bMelUnd1.mat - Sequences = 930 - Bases = 1169393027 - N50 = 79295844 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 110188325-118058829 | [ 2 ] 102317821-110188324 | [ ] 94447317-102317820 | [ ] 86576813-94447316 | [ 3 ] 78706309-86576812 | [ 1 ] 70835805-78706308 | [ 1 ] 62965301-70835804 | [ ] 55094798-62965301 | [ 2 ] 47224294-55094797 | [ ] 39353790-47224293 | [ 1 ] 31483286-39353789 | [ 2 ] 23612782-31483285 | [ 2 ] 15742278-23612781 | [ 3 ] 7871774-15742277 | [ 1 ] 1271-7871774 |************************************************** [ 912 ] Storage Throughput = excellent ( 1193.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42330141 bp ( 40013961 non ambiguous ) - Num Contigs Represented = 120 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:41 (hh:mm:ss) Elapsed Time Round Time: 00:29:42 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3397 repeats masked totaling 1029839 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10497248 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10039362 bp After Masking: 8736767 bp Masked: 12.97 % -- Input Database Coverage: 10497248 bp out of 1169393027 bp ( 0.90 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:06:35 (hh:mm:ss) Elapsed Time, 264 HSPs Collected Number of families returned by RECON: 164 Round Time: 00:07:46 (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 : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9317 repeats masked totaling 2879747 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31872894 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 30014600 bp After Masking: 26330105 bp Masked: 12.28 % -- Input Database Coverage: 42370142 bp out of 1169393027 bp ( 3.62 % ) Sampling Time: 00:05:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 327645 Comparison Time: 00:52:25 (hh:mm:ss) Elapsed Time, 7352 HSPs Collected Number of families returned by RECON: 1307 Round Time: 00:57:55 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32822 repeats masked totaling 9321304 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95598982 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 90024606 bp After Masking: 78912429 bp Masked: 12.34 % -- Input Database Coverage: 137969124 bp out of 1169393027 bp ( 11.80 % ) Sampling Time: 00:09:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2970703 Comparison Time: 04:42:43 (hh:mm:ss) Elapsed Time, 46852 HSPs Collected Number of families returned by RECON: 8995 Round Time: 04:56:08 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107470 repeats masked totaling 30191655 bp(s). - TE Masking time 00:03:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 287045011 bp Num Contigs Represented = 412 Non ambiguous bp: Initial: 270029528 bp After Masking: 234554778 bp Masked: 13.14 % -- Input Database Coverage: 425014135 bp out of 1169393027 bp ( 36.34 % ) Sampling Time: 00:30:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26619456 Comparison Time: 36:42:50 (hh:mm:ss) Elapsed Time, 220605 HSPs Collected Number of families returned by RECON: 60848 Round Time: 38:06:58 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatScout/RECON discovery complete: 350 families found Classification Time: 00:39:02 (hh:mm:ss) Elapsed Time Program Time: 45:17:31 (hh:mm:ss) Elapsed Time