RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ubzyZT/RM_3267956.WedDec61301252023 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: 1701896484 Database = /dev/shm/rModeler.ubzyZT/GCA_963280865.1_fGymBra2.1 - Sequences = 676 - Bases = 1367984568 - N50 = 55997761 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61841073-66258222 | [ 2 ] 57423925-61841073 | [ 5 ] 53006777-57423925 | [ 8 ] 48589629-53006777 | [ 5 ] 44172481-48589629 | [ 2 ] 39755333-44172481 | [ 2 ] 35338185-39755333 | [ ] 30921036-35338184 | [ ] 26503888-30921036 | [ ] 22086740-26503888 | [ ] 17669592-22086740 | [ ] 13252444-17669592 | [ ] 8835296-13252444 | [ ] 4418148-8835296 | [ ] 1000-4418148 |************************************************** [ 652 ] Storage Throughput = excellent ( 1133.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040017 bp ( 40022524 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:24 (hh:mm:ss) Elapsed Time Round Time: 00:29:05 (hh:mm:ss) Elapsed Time : 1087 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26771 repeats masked totaling 3512524 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018116 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10013672 bp After Masking: 5595112 bp Masked: 44.13 % -- Input Database Coverage: 10018116 bp out of 1367984568 bp ( 0.73 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:34 (hh:mm:ss) Elapsed Time, 6473 HSPs Collected Number of families returned by RECON: 1627 Round Time: 00:09:25 (hh:mm:ss) Elapsed Time : 12 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 00:03:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80897 repeats masked totaling 10748013 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021897 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 30008848 bp After Masking: 16549725 bp Masked: 44.85 % -- Input Database Coverage: 40040013 bp out of 1367984568 bp ( 2.93 % ) Sampling Time: 00:05:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:27:18 (hh:mm:ss) Elapsed Time, 53373 HSPs Collected Number of families returned by RECON: 6053 Round Time: 00:35:32 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 247616 repeats masked totaling 32678124 bp(s). - TE Masking time 00:03:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90063600 bp Num Contigs Represented = 135 Non ambiguous bp: Initial: 90029599 bp After Masking: 48984432 bp Masked: 45.59 % -- Input Database Coverage: 130103613 bp out of 1367984568 bp ( 9.51 % ) Sampling Time: 00:16:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 02:44:16 (hh:mm:ss) Elapsed Time, 396402 HSPs Collected Number of families returned by RECON: 19166 Round Time: 03:20:32 (hh:mm:ss) Elapsed Time : 741 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 837765 repeats masked totaling 114508157 bp(s). - TE Masking time 00:15:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270118081 bp Num Contigs Represented = 283 Non ambiguous bp: Initial: 270012526 bp After Masking: 131326533 bp Masked: 51.36 % -- Input Database Coverage: 400221694 bp out of 1367984568 bp ( 29.26 % ) Sampling Time: 00:54:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 18:09:58 (hh:mm:ss) Elapsed Time, 1434962 HSPs Collected Number of families returned by RECON: 54827 Round Time: 20:51:59 (hh:mm:ss) Elapsed Time : 2009 families discovered. RepeatScout/RECON discovery complete: 3972 families found Classification Time: 02:38:13 (hh:mm:ss) Elapsed Time Program Time: 28:04:46 (hh:mm:ss) Elapsed Time