RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PL3A5Z/RM_318322.ThuApr171001342025 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: 1744909291 Database = /dev/shm/rModeler.PL3A5Z/GCA_964656465.1_mHalGry1.hap2.1 - Sequences = 123 - Bases = 2387143391 - N50 = 187763404 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203165183-217676931 |* [ 3 ] 188653436-203165183 | [ 1 ] 174141688-188653435 | [ 2 ] 159629941-174141688 | [ ] 145118194-159629941 |* [ 3 ] 130606446-145118193 | [ 1 ] 116094699-130606446 | [ 1 ] 101582951-116094698 | [ 2 ] 87071204-101582951 | [ 2 ] 72559457-87071204 | [ ] 58047709-72559456 | [ 1 ] 43535962-58047709 | [ ] 29024214-43535961 | [ ] 14512467-29024214 | [ ] 720-14512467 |************************************************** [ 107 ] Storage Throughput = excellent ( 1815.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013311 bp ( 40010311 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:12 (hh:mm:ss) Elapsed Time Round Time: 00:13:53 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10566 repeats masked totaling 2303310 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000988 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10000588 bp After Masking: 7579986 bp Masked: 24.20 % -- Input Database Coverage: 10000988 bp out of 2387143391 bp ( 0.42 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 29026 HSPs Collected Number of families returned by RECON: 877 Round Time: 00:04:04 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36267 repeats masked totaling 7821405 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012243 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30009643 bp After Masking: 21903505 bp Masked: 27.01 % -- Input Database Coverage: 40013231 bp out of 2387143391 bp ( 1.68 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:13:18 (hh:mm:ss) Elapsed Time, 60411 HSPs Collected Number of families returned by RECON: 2680 Round Time: 00:15:41 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 119595 repeats masked totaling 27006147 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025971 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90018571 bp After Masking: 61989706 bp Masked: 31.14 % -- Input Database Coverage: 130039202 bp out of 2387143391 bp ( 5.45 % ) Sampling Time: 00:05:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:17:18 (hh:mm:ss) Elapsed Time, 508758 HSPs Collected Number of families returned by RECON: 9583 Round Time: 01:24:48 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 396130 repeats masked totaling 87159310 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032556 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 270004993 bp After Masking: 180224284 bp Masked: 33.25 % -- Input Database Coverage: 400071758 bp out of 2387143391 bp ( 16.76 % ) Sampling Time: 00:18:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 08:58:06 (hh:mm:ss) Elapsed Time, 3477061 HSPs Collected Number of families returned by RECON: 38711 Round Time: 09:28:16 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatScout/RECON discovery complete: 814 families found Classification Time: 00:14:40 (hh:mm:ss) Elapsed Time Program Time: 11:41:22 (hh:mm:ss) Elapsed Time