RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.aPUDVK/RM_631146.FriMay120850542023 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: 1683906653 Database = /dev/shm/rModeler.aPUDVK/GCA_028022725.1_fLycPai1.hap2 - Sequences = 109 - Bases = 646369862 - N50 = 28913003 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31698008-33962080 |* [ 3 ] 29433936-31698008 |** [ 4 ] 27169864-29433936 |** [ 5 ] 24905792-27169864 |* [ 3 ] 22641720-24905792 |** [ 4 ] 20377648-22641720 |* [ 2 ] 18113576-20377648 |* [ 2 ] 15849504-18113576 | [ ] 13585432-15849504 | [ 1 ] 11321360-13585432 | [ ] 9057288-11321360 | [ ] 6793216-9057288 | [ ] 4529144-6793216 | [ ] 2265072-4529144 | [ ] 1000-2265072 |************************************************** [ 85 ] Storage Throughput = excellent ( 1178.32 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042517 bp ( 40037917 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:16 (hh:mm:ss) Elapsed Time Round Time: 00:21:28 (hh:mm:ss) Elapsed Time : 474 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6583 repeats masked totaling 1378676 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025906 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10024506 bp After Masking: 7759274 bp Masked: 22.60 % -- Input Database Coverage: 10025906 bp out of 646369862 bp ( 1.55 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:26 (hh:mm:ss) Elapsed Time, 7918 HSPs Collected Number of families returned by RECON: 1191 Round Time: 00:10:19 (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 : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21005 repeats masked totaling 4192095 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016531 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30013331 bp After Masking: 23529793 bp Masked: 21.60 % -- Input Database Coverage: 40042437 bp out of 646369862 bp ( 6.19 % ) Sampling Time: 00:05:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:33:44 (hh:mm:ss) Elapsed Time, 60474 HSPs Collected Number of families returned by RECON: 4863 Round Time: 00:45:17 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73137 repeats masked totaling 14495770 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020091 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90011891 bp After Masking: 69531991 bp Masked: 22.75 % -- Input Database Coverage: 130062528 bp out of 646369862 bp ( 20.12 % ) Sampling Time: 00:17:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:15:49 (hh:mm:ss) Elapsed Time, 401757 HSPs Collected Number of families returned by RECON: 17785 Round Time: 03:48:08 (hh:mm:ss) Elapsed Time : 412 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 280624 repeats masked totaling 54922446 bp(s). - TE Masking time 00:09:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040760 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 270005160 bp After Masking: 195893819 bp Masked: 27.45 % -- Input Database Coverage: 400103288 bp out of 646369862 bp ( 61.90 % ) Sampling Time: 01:04:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 23:59:24 (hh:mm:ss) Elapsed Time, 1579802 HSPs Collected Number of families returned by RECON: 67282 Round Time: 27:02:47 (hh:mm:ss) Elapsed Time : 1051 families discovered. RepeatScout/RECON discovery complete: 2055 families found Classification Time: 02:03:45 (hh:mm:ss) Elapsed Time Program Time: 34:11:44 (hh:mm:ss) Elapsed Time