RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3BHNvd/RM_77675.MonJan92154502023 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: 1673330089 Database = /dev/shm/rModeler.3BHNvd/GCA_025201965.1_rGopFla2.pat.asm - Sequences = 2992 - Bases = 2584697711 - N50 = 139571378 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 212343822-227511160 | [ 1 ] 197176485-212343822 | [ ] 182009148-197176485 | [ 1 ] 166841811-182009148 | [ 1 ] 151674474-166841811 | [ ] 136507136-151674473 | [ 4 ] 121339799-136507136 | [ 2 ] 106172462-121339799 | [ 1 ] 91005125-106172462 | [ 1 ] 75837788-91005125 | [ 1 ] 60670450-75837787 | [ 1 ] 45503113-60670450 | [ ] 30335776-45503113 | [ 6 ] 15168439-30335776 | [ 9 ] 1102-15168439 |************************************************** [ 2964 ] Storage Throughput = excellent ( 1673.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41457091 bp ( 40027614 non ambiguous ) - Num Contigs Represented = 132 - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:14 (hh:mm:ss) Elapsed Time Round Time: 00:22:08 (hh:mm:ss) Elapsed Time : 586 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13415 repeats masked totaling 3496218 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10276956 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10000175 bp After Masking: 6281143 bp Masked: 37.19 % -- Input Database Coverage: 10276956 bp out of 2584697711 bp ( 0.40 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:59 (hh:mm:ss) Elapsed Time, 14800 HSPs Collected Number of families returned by RECON: 1607 Round Time: 00:07:45 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43082 repeats masked totaling 10623912 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31180055 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 30027359 bp After Masking: 18874889 bp Masked: 37.14 % -- Input Database Coverage: 41457011 bp out of 2584697711 bp ( 1.60 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 314028 Comparison Time: 00:22:24 (hh:mm:ss) Elapsed Time, 60828 HSPs Collected Number of families returned by RECON: 4640 Round Time: 00:26:36 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143215 repeats masked totaling 34676118 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94616504 bp Num Contigs Represented = 281 Non ambiguous bp: Initial: 90003093 bp After Masking: 53743340 bp Masked: 40.29 % -- Input Database Coverage: 136073515 bp out of 2584697711 bp ( 5.26 % ) Sampling Time: 00:09:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2943951 Comparison Time: 02:01:51 (hh:mm:ss) Elapsed Time, 219628 HSPs Collected Number of families returned by RECON: 13082 Round Time: 02:18:19 (hh:mm:ss) Elapsed Time : 420 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 499335 repeats masked totaling 118170075 bp(s). - TE Masking time 00:07:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 283761559 bp Num Contigs Represented = 673 Non ambiguous bp: Initial: 270015909 bp After Masking: 146708884 bp Masked: 45.67 % -- Input Database Coverage: 419835074 bp out of 2584697711 bp ( 16.24 % ) Sampling Time: 00:39:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26386480 Comparison Time: 12:17:06 (hh:mm:ss) Elapsed Time, 598798 HSPs Collected Number of families returned by RECON: 40044 Round Time: 13:34:58 (hh:mm:ss) Elapsed Time : 976 families discovered. RepeatScout/RECON discovery complete: 2132 families found Classification Time: 01:04:54 (hh:mm:ss) Elapsed Time Program Time: 17:54:40 (hh:mm:ss) Elapsed Time