RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jMiQTE/RM_684557.WedApr230530402025 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: 1745411440 Database = /dev/shm/rModeler.jMiQTE/GCA_048129055.1_fCaeTer1.1_haplotype_1 - Sequences = 323 - Bases = 1078118487 - N50 = 43361379 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61536793-65931628 | [ 1 ] 57141959-61536793 | [ ] 52747124-57141958 | [ ] 48352290-52747124 | [ 4 ] 43957455-48352289 | [ 5 ] 39562621-43957455 |* [ 6 ] 35167786-39562620 | [ 4 ] 30772952-35167786 | [ 2 ] 26378117-30772951 | [ 1 ] 21983283-26378117 | [ ] 17588448-21983282 | [ ] 13193614-17588448 | [ ] 8798779-13193613 | [ ] 4403945-8798779 | [ ] 9111-4403945 |************************************************** [ 300 ] Storage Throughput = excellent ( 1697.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002704 bp ( 40002704 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:07 (hh:mm:ss) Elapsed Time Round Time: 00:12:34 (hh:mm:ss) Elapsed Time : 786 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17325 repeats masked totaling 2330986 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003066 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10003066 bp After Masking: 7331997 bp Masked: 26.70 % -- Input Database Coverage: 10003066 bp out of 1078118487 bp ( 0.93 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:08 (hh:mm:ss) Elapsed Time, 17749 HSPs Collected Number of families returned by RECON: 2333 Round Time: 00:03:55 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54565 repeats masked totaling 7921583 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039575 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 30039575 bp After Masking: 20994108 bp Masked: 30.11 % -- Input Database Coverage: 40042641 bp out of 1078118487 bp ( 3.71 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:14:28 (hh:mm:ss) Elapsed Time, 100450 HSPs Collected Number of families returned by RECON: 6927 Round Time: 00:17:19 (hh:mm:ss) Elapsed Time : 265 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189133 repeats masked totaling 27297714 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034395 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 90033995 bp After Masking: 59249020 bp Masked: 34.19 % -- Input Database Coverage: 130077036 bp out of 1078118487 bp ( 12.07 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:20:49 (hh:mm:ss) Elapsed Time, 378168 HSPs Collected Number of families returned by RECON: 19048 Round Time: 01:31:45 (hh:mm:ss) Elapsed Time : 650 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 665203 repeats masked totaling 99357288 bp(s). - TE Masking time 00:04:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038337 bp Num Contigs Represented = 219 Non ambiguous bp: Initial: 270037337 bp After Masking: 160352625 bp Masked: 40.62 % -- Input Database Coverage: 400115373 bp out of 1078118487 bp ( 37.11 % ) Sampling Time: 00:14:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 08:17:00 (hh:mm:ss) Elapsed Time, 985153 HSPs Collected Number of families returned by RECON: 59905 Round Time: 09:11:39 (hh:mm:ss) Elapsed Time : 1553 families discovered. RepeatScout/RECON discovery complete: 3310 families found Classification Time: 00:57:57 (hh:mm:ss) Elapsed Time Program Time: 12:15:09 (hh:mm:ss) Elapsed Time