RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.xaXNAZ/RM_2461025.FriNov152237102024 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: 1731739029 Database = /scratch/tmp/rModeler.xaXNAZ/GCF_036365525.1_sHetFra1.hap1 - Sequences = 2306 - Bases = 6013048672 - N50 = 93226506 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 268750874-287946412 | [ 1 ] 249555336-268750873 | [ ] 230359799-249555336 | [ ] 211164261-230359798 | [ 3 ] 191968724-211164261 | [ 1 ] 172773186-191968723 | [ ] 153577649-172773186 | [ 1 ] 134382111-153577648 | [ 2 ] 115186574-134382111 | [ 5 ] 95991036-115186573 | [ 5 ] 76795499-95991036 | [ 8 ] 57599961-76795498 | [ 9 ] 38404424-57599961 | [ 6 ] 19208886-38404423 | [ 9 ] 13349-19208886 |************************************************** [ 2256 ] Storage Throughput = excellent ( 1576.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40312299 bp ( 40009442 non ambiguous ) - Num Contigs Represented = 242 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:23 (hh:mm:ss) Elapsed Time Round Time: 00:17:03 (hh:mm:ss) Elapsed Time : 578 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14718 repeats masked totaling 4960955 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10139329 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 10021826 bp After Masking: 2148804 bp Masked: 78.56 % -- Input Database Coverage: 10139329 bp out of 6013048672 bp ( 0.17 % ) Sampling Time: 00:06:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:02:45 (hh:mm:ss) Elapsed Time, 5922 HSPs Collected Number of families returned by RECON: 549 Round Time: 00:09:30 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45514 repeats masked totaling 14886498 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30212890 bp Num Contigs Represented = 195 Non ambiguous bp: Initial: 30027536 bp After Masking: 7088909 bp Masked: 76.39 % -- Input Database Coverage: 40352219 bp out of 6013048672 bp ( 0.67 % ) Sampling Time: 00:18:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:09:26 (hh:mm:ss) Elapsed Time, 26553 HSPs Collected Number of families returned by RECON: 2027 Round Time: 00:28:49 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140589 repeats masked totaling 45399157 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90448799 bp Num Contigs Represented = 390 Non ambiguous bp: Initial: 90012692 bp After Masking: 19746557 bp Masked: 78.06 % -- Input Database Coverage: 130801018 bp out of 6013048672 bp ( 2.18 % ) Sampling Time: 00:56:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 00:39:11 (hh:mm:ss) Elapsed Time, 127886 HSPs Collected Number of families returned by RECON: 5005 Round Time: 01:37:49 (hh:mm:ss) Elapsed Time : 231 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:39:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 446046 repeats masked totaling 143905456 bp(s). - TE Masking time 00:03:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271240731 bp Num Contigs Represented = 743 Non ambiguous bp: Initial: 270016894 bp After Masking: 51676572 bp Masked: 80.86 % -- Input Database Coverage: 402041749 bp out of 6013048672 bp ( 6.69 % ) Sampling Time: 02:49:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 03:27:54 (hh:mm:ss) Elapsed Time, 383006 HSPs Collected Number of families returned by RECON: 12954 Round Time: 06:30:22 (hh:mm:ss) Elapsed Time : 522 families discovered. RepeatScout/RECON discovery complete: 1393 families found Classification Time: 00:31:06 (hh:mm:ss) Elapsed Time Program Time: 09:34:40 (hh:mm:ss) Elapsed Time