RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.C6tIvB/RM_1549329.MonJul151325252024 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: 1721075124 Database = /dev/shm/rModeler.C6tIvB/GCF_025434085.1_ASM2543408v3 - Sequences = 213 - Bases = 544521268 - N50 = 26402226 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 40075984-42937977 | [ 2 ] 37213991-40075983 | [ ] 34351999-37213991 | [ ] 31490006-34351998 | [ ] 28628014-31490006 | [ 3 ] 25766021-28628013 |* [ 5 ] 22904028-25766020 |* [ 4 ] 20042036-22904028 | [ 1 ] 17180043-20042035 | [ 3 ] 14318051-17180043 | [ ] 11456058-14318050 | [ 2 ] 8594065-11456057 | [ 1 ] 5732073-8594065 | [ ] 2870080-5732072 | [ 1 ] 8088-2870080 |************************************************** [ 191 ] Storage Throughput = excellent ( 1071.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033668 bp ( 40033508 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:16 (hh:mm:ss) Elapsed Time Round Time: 00:37:00 (hh:mm:ss) Elapsed Time : 351 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8343 repeats masked totaling 2039740 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004527 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10004507 bp After Masking: 6618445 bp Masked: 33.85 % -- Input Database Coverage: 10004527 bp out of 544521268 bp ( 1.84 % ) Sampling Time: 00:03:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:15 (hh:mm:ss) Elapsed Time, 7200 HSPs Collected Number of families returned by RECON: 1258 Round Time: 00:10:28 (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 : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27336 repeats masked totaling 7045871 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029136 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30028996 bp After Masking: 20127537 bp Masked: 32.97 % -- Input Database Coverage: 40033663 bp out of 544521268 bp ( 7.35 % ) Sampling Time: 00:04:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:30:39 (hh:mm:ss) Elapsed Time, 46433 HSPs Collected Number of families returned by RECON: 4690 Round Time: 00:36:45 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 98009 repeats masked totaling 23599379 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010006 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90009806 bp After Masking: 56713601 bp Masked: 36.99 % -- Input Database Coverage: 130043669 bp out of 544521268 bp ( 23.88 % ) Sampling Time: 00:14:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 02:46:12 (hh:mm:ss) Elapsed Time, 201994 HSPs Collected Number of families returned by RECON: 14739 Round Time: 03:08:06 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 358696 repeats masked totaling 83193499 bp(s). - TE Masking time 00:06:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030075 bp Num Contigs Represented = 142 Non ambiguous bp: Initial: 270029275 bp After Masking: 157260318 bp Masked: 41.76 % -- Input Database Coverage: 400073744 bp out of 544521268 bp ( 73.47 % ) Sampling Time: 00:39:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 26:36:52 (hh:mm:ss) Elapsed Time, 540182 HSPs Collected Number of families returned by RECON: 51597 Round Time: 28:19:41 (hh:mm:ss) Elapsed Time : 791 families discovered. RepeatScout/RECON discovery complete: 1700 families found Classification Time: 01:00:54 (hh:mm:ss) Elapsed Time Program Time: 33:52:54 (hh:mm:ss) Elapsed Time