RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4HUHjU/RM_359427.FriJan270929412023 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: 1674840578 Database = /dev/shm/rModeler.4HUHjU/GCF_009764475.1_sPriPec2.1.pri - Sequences = 172 - Bases = 2267840987 - N50 = 102490209 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 139971069-149968914 |* [ 3 ] 129973224-139971068 | [ ] 119975379-129973223 | [ 1 ] 109977534-119975378 | [ 2 ] 99979690-109977534 |* [ 4 ] 89981845-99979689 | [ ] 79984000-89981844 | [ 1 ] 69986155-79983999 | [ ] 59988310-69986154 | [ ] 49990466-59988310 |* [ 4 ] 39992621-49990465 |* [ 5 ] 29994776-39992620 |*** [ 8 ] 19996931-29994775 |* [ 5 ] 9999086-19996930 |** [ 6 ] 1242-9999086 |************************************************** [ 133 ] Storage Throughput = excellent ( 1301.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40474889 bp ( 40021709 non ambiguous ) - Num Contigs Represented = 50 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:02 (hh:mm:ss) Elapsed Time Round Time: 00:14:44 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18309 repeats masked totaling 4129720 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10122030 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10034824 bp After Masking: 5792245 bp Masked: 42.28 % -- Input Database Coverage: 10122030 bp out of 2267840987 bp ( 0.45 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:09:09 (hh:mm:ss) Elapsed Time, 6142 HSPs Collected Number of families returned by RECON: 910 Round Time: 00:10:14 (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 : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60853 repeats masked totaling 13825109 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30392789 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30026815 bp After Masking: 15878638 bp Masked: 47.12 % -- Input Database Coverage: 40514819 bp out of 2267840987 bp ( 1.79 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:30:18 (hh:mm:ss) Elapsed Time, 26936 HSPs Collected Number of families returned by RECON: 2711 Round Time: 00:33:37 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 192641 repeats masked totaling 43413607 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90954757 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90036923 bp After Masking: 45739352 bp Masked: 49.20 % -- Input Database Coverage: 131469576 bp out of 2267840987 bp ( 5.80 % ) Sampling Time: 00:07:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 02:46:06 (hh:mm:ss) Elapsed Time, 88733 HSPs Collected Number of families returned by RECON: 7450 Round Time: 02:56:22 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 616076 repeats masked totaling 138649663 bp(s). - TE Masking time 00:04:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272461608 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270005410 bp After Masking: 128400767 bp Masked: 52.45 % -- Input Database Coverage: 403931184 bp out of 2267840987 bp ( 17.81 % ) Sampling Time: 00:24:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23232336 Comparison Time: 13:59:43 (hh:mm:ss) Elapsed Time, 242952 HSPs Collected Number of families returned by RECON: 25871 Round Time: 14:37:22 (hh:mm:ss) Elapsed Time : 461 families discovered. RepeatScout/RECON discovery complete: 1038 families found Classification Time: 00:28:45 (hh:mm:ss) Elapsed Time Program Time: 19:01:04 (hh:mm:ss) Elapsed Time