RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.4tMsQa/RM_2180483.WedDec40407072024 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: 1733314027 Database = /scratch/tmp/rModeler.4tMsQa/GCA_964264895.1_mNycLei1.hap2.1 - Sequences = 1335 - Bases = 2011002017 - N50 = 89247453 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203578870-218120147 | [ 1 ] 189037594-203578870 | [ 2 ] 174496317-189037593 | [ ] 159955041-174496317 | [ ] 145413764-159955040 | [ ] 130872488-145413764 | [ ] 116331211-130872487 | [ ] 101789935-116331211 | [ 2 ] 87248658-101789934 | [ 2 ] 72707382-87248658 | [ 4 ] 58166105-72707381 | [ 2 ] 43624829-58166105 | [ 4 ] 29083552-43624828 | [ 1 ] 14542276-29083552 | [ 2 ] 1000-14542276 |************************************************** [ 1315 ] Storage Throughput = excellent ( 1536.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041808 bp ( 40036208 non ambiguous ) - Num Contigs Represented = 136 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:33 (hh:mm:ss) Elapsed Time Round Time: 00:13:41 (hh:mm:ss) Elapsed Time : 377 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 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14873 repeats masked totaling 2695004 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007033 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10005433 bp After Masking: 6430804 bp Masked: 35.73 % -- Input Database Coverage: 10007033 bp out of 2011002017 bp ( 0.50 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:03:03 (hh:mm:ss) Elapsed Time, 3045 HSPs Collected Number of families returned by RECON: 610 Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46513 repeats masked totaling 8334307 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034695 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 30030695 bp After Masking: 19382961 bp Masked: 35.46 % -- Input Database Coverage: 40041728 bp out of 2011002017 bp ( 1.99 % ) Sampling Time: 00:03:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:13:41 (hh:mm:ss) Elapsed Time, 41670 HSPs Collected Number of families returned by RECON: 2538 Round Time: 00:18:14 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152424 repeats masked totaling 27303385 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90050377 bp Num Contigs Represented = 232 Non ambiguous bp: Initial: 90033927 bp After Masking: 55902333 bp Masked: 37.91 % -- Input Database Coverage: 130092105 bp out of 2011002017 bp ( 6.47 % ) Sampling Time: 00:11:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 01:17:46 (hh:mm:ss) Elapsed Time, 97839 HSPs Collected Number of families returned by RECON: 7263 Round Time: 01:30:35 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 482705 repeats masked totaling 89204241 bp(s). - TE Masking time 00:04:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066929 bp Num Contigs Represented = 469 Non ambiguous bp: Initial: 270031190 bp After Masking: 158898813 bp Masked: 41.16 % -- Input Database Coverage: 400159034 bp out of 2011002017 bp ( 19.90 % ) Sampling Time: 00:35:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 08:18:11 (hh:mm:ss) Elapsed Time, 260013 HSPs Collected Number of families returned by RECON: 28925 Round Time: 09:02:40 (hh:mm:ss) Elapsed Time : 425 families discovered. RepeatScout/RECON discovery complete: 1062 families found Classification Time: 00:32:39 (hh:mm:ss) Elapsed Time Program Time: 11:42:10 (hh:mm:ss) Elapsed Time