RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CVrquy/RM_2798781.WedApr231028242025 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: 1745429304 Database = /dev/shm/rModeler.CVrquy/GCA_049082185.1_fCriAus1.1_haplotype_1 - Sequences = 793 - Bases = 619674967 - N50 = 27384081 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35869365-38431221 | [ 1 ] 33307510-35869365 | [ ] 30745655-33307510 | [ ] 28183799-30745654 | [ 5 ] 25621944-28183799 | [ 6 ] 23060089-25621944 | [ 2 ] 20498234-23060089 | [ 4 ] 17936378-20498233 | [ 3 ] 15374523-17936378 | [ 1 ] 12812668-15374523 | [ 1 ] 10250813-12812668 | [ ] 7688957-10250812 | [ 1 ] 5127102-7688957 | [ ] 2565247-5127102 | [ 1 ] 3392-2565247 |************************************************** [ 768 ] Storage Throughput = excellent ( 1641.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40054462 bp ( 40034296 non ambiguous ) - Num Contigs Represented = 96 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:09 (hh:mm:ss) Elapsed Time Round Time: 00:11:45 (hh:mm:ss) Elapsed Time : 349 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6443 repeats masked totaling 1109872 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020286 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10013686 bp After Masking: 8299168 bp Masked: 17.12 % -- Input Database Coverage: 10020286 bp out of 619674967 bp ( 1.62 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:20 (hh:mm:ss) Elapsed Time, 5291 HSPs Collected Number of families returned by RECON: 1033 Round Time: 00:04:24 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19088 repeats masked totaling 3202474 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034159 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30020593 bp After Masking: 24846668 bp Masked: 17.23 % -- Input Database Coverage: 40054445 bp out of 619674967 bp ( 6.46 % ) Sampling Time: 00:02:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:16:34 (hh:mm:ss) Elapsed Time, 30890 HSPs Collected Number of families returned by RECON: 4273 Round Time: 00:19:18 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61118 repeats masked totaling 9852387 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90060524 bp Num Contigs Represented = 193 Non ambiguous bp: Initial: 90028850 bp After Masking: 73961254 bp Masked: 17.85 % -- Input Database Coverage: 130114969 bp out of 619674967 bp ( 21.00 % ) Sampling Time: 00:07:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2666895 Comparison Time: 01:41:40 (hh:mm:ss) Elapsed Time, 201730 HSPs Collected Number of families returned by RECON: 18024 Round Time: 01:53:26 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 229651 repeats masked totaling 38390047 bp(s). - TE Masking time 00:02:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270121144 bp Num Contigs Represented = 430 Non ambiguous bp: Initial: 270020588 bp After Masking: 213053847 bp Masked: 21.10 % -- Input Database Coverage: 400236113 bp out of 619674967 bp ( 64.59 % ) Sampling Time: 00:25:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24008985 Comparison Time: 12:14:52 (hh:mm:ss) Elapsed Time, 698070 HSPs Collected Number of families returned by RECON: 73758 Round Time: 13:20:53 (hh:mm:ss) Elapsed Time : 784 families discovered. RepeatScout/RECON discovery complete: 1465 families found Classification Time: 00:38:16 (hh:mm:ss) Elapsed Time Program Time: 16:28:02 (hh:mm:ss) Elapsed Time