RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FOXTCZ/RM_20791.WedJul30712032024 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: 1720015922 Database = /dev/shm/rModeler.FOXTCZ/GCF_000238955.4_M_zebra_UMD2a - Sequences = 1690 - Bases = 957485262 - N50 = 34086040 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 60589392-64916660 | [ 1 ] 56262124-60589391 | [ ] 51934857-56262124 | [ ] 47607589-51934856 | [ ] 43280321-47607588 | [ ] 38953054-43280321 | [ 2 ] 34625786-38953053 | [ 7 ] 30298518-34625785 | [ 7 ] 25971251-30298518 | [ 2 ] 21643983-25971250 | [ 2 ] 17316715-21643982 | [ 1 ] 12989448-17316715 | [ ] 8662180-12989447 | [ ] 4334912-8662179 | [ ] 7645-4334912 |************************************************** [ 1668 ] Storage Throughput = excellent ( 1039.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036224 bp ( 40033024 non ambiguous ) - Num Contigs Represented = 231 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:07 (hh:mm:ss) Elapsed Time Round Time: 00:26:42 (hh:mm:ss) Elapsed Time : 700 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 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10413 repeats masked totaling 2668250 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001872 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 10000672 bp After Masking: 7158309 bp Masked: 28.42 % -- Input Database Coverage: 10001872 bp out of 957485262 bp ( 1.04 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:05:16 (hh:mm:ss) Elapsed Time, 6859 HSPs Collected Number of families returned by RECON: 1220 Round Time: 00:06:33 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32564 repeats masked totaling 8075293 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034272 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 30032272 bp After Masking: 21522326 bp Masked: 28.34 % -- Input Database Coverage: 40036144 bp out of 957485262 bp ( 4.18 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 300700 Comparison Time: 00:28:52 (hh:mm:ss) Elapsed Time, 48426 HSPs Collected Number of families returned by RECON: 4425 Round Time: 00:33:06 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107495 repeats masked totaling 25031909 bp(s). - TE Masking time 00:02:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045235 bp Num Contigs Represented = 429 Non ambiguous bp: Initial: 90039135 bp After Masking: 63554589 bp Masked: 29.41 % -- Input Database Coverage: 130081379 bp out of 957485262 bp ( 13.59 % ) Sampling Time: 00:08:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2692360 Comparison Time: 03:27:17 (hh:mm:ss) Elapsed Time, 265988 HSPs Collected Number of families returned by RECON: 14456 Round Time: 03:50:08 (hh:mm:ss) Elapsed Time : 396 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 374359 repeats masked totaling 88332194 bp(s). - TE Masking time 00:14:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270050533 bp Num Contigs Represented = 932 Non ambiguous bp: Initial: 270034733 bp After Masking: 177426707 bp Masked: 34.29 % -- Input Database Coverage: 400131912 bp out of 957485262 bp ( 41.79 % ) Sampling Time: 00:32:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24384636 Comparison Time: 26:20:13 (hh:mm:ss) Elapsed Time, 709266 HSPs Collected Number of families returned by RECON: 49739 Round Time: 28:21:05 (hh:mm:ss) Elapsed Time : 1071 families discovered. RepeatScout/RECON discovery complete: 2276 families found Classification Time: 02:33:19 (hh:mm:ss) Elapsed Time Program Time: 35:50:53 (hh:mm:ss) Elapsed Time