RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UI6Dkr/RM_19868.FriFeb71220082025 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: 1738959580 Database = /dev/shm/rModeler.UI6Dkr/GCA_045364795.1_bWilVid1_haplotype_1 - Sequences = 1510 - Bases = 1233406177 - N50 = 78812073 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 117257448-125632909 | [ 2 ] 108881987-117257447 | [ ] 100506527-108881987 | [ 1 ] 92131066-100506526 | [ ] 83755606-92131066 | [ ] 75380145-83755605 | [ 3 ] 67004684-75380144 | [ 1 ] 58629224-67004684 | [ 1 ] 50253763-58629223 | [ 2 ] 41878303-50253763 | [ ] 33502842-41878302 | [ ] 25127381-33502841 | [ 2 ] 16751921-25127381 | [ 6 ] 8376460-16751920 | [ 5 ] 1000-8376460 |************************************************** [ 1487 ] Storage Throughput = excellent ( 1902.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038653 bp ( 40033653 non ambiguous ) - Num Contigs Represented = 123 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:51 (hh:mm:ss) Elapsed Time Round Time: 00:39:09 (hh:mm:ss) Elapsed Time : 145 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3848 repeats masked totaling 1248684 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009395 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 10008195 bp After Masking: 8099254 bp Masked: 19.07 % -- Input Database Coverage: 10009395 bp out of 1233406177 bp ( 0.81 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 01:57:36 (hh:mm:ss) Elapsed Time, 1031 HSPs Collected Number of families returned by RECON: 302 Round Time: 01:59:09 (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 : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10374 repeats masked totaling 3025526 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029257 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 30025457 bp After Masking: 24600967 bp Masked: 18.07 % -- Input Database Coverage: 40038652 bp out of 1233406177 bp ( 3.25 % ) Sampling Time: 00:02:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 05:50:56 (hh:mm:ss) Elapsed Time, 5951 HSPs Collected Number of families returned by RECON: 1486 Round Time: 05:57:56 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31545 repeats masked totaling 9365369 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011875 bp Num Contigs Represented = 230 Non ambiguous bp: Initial: 90000875 bp After Masking: 73635118 bp Masked: 18.18 % -- Input Database Coverage: 130050527 bp out of 1233406177 bp ( 10.54 % ) Sampling Time: 00:07:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2662278 Comparison Time: 18:25:25 (hh:mm:ss) Elapsed Time, 55435 HSPs Collected Number of families returned by RECON: 9083 Round Time: 18:48:00 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105604 repeats masked totaling 32634422 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041089 bp Num Contigs Represented = 562 Non ambiguous bp: Initial: 270007489 bp After Masking: 215865016 bp Masked: 20.05 % -- Input Database Coverage: 400091616 bp out of 1233406177 bp ( 32.44 % ) Sampling Time: 00:20:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24189490 Comparison Time: 41:19:42 (hh:mm:ss) Elapsed Time, 221854 HSPs Collected Number of families returned by RECON: 58928 Round Time: 41:57:59 (hh:mm:ss) Elapsed Time : 254 families discovered. RepeatScout/RECON discovery complete: 502 families found Classification Time: 00:17:11 (hh:mm:ss) Elapsed Time Program Time: 69:39:24 (hh:mm:ss) Elapsed Time