RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rhxSCp/RM_2195169.MonDec40226312023 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: 1701685591 Database = /dev/shm/rModeler.rhxSCp/GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b - Sequences = 214 - Bases = 1053332251 - N50 = 110642502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 183352641-196449156 | [ 1 ] 170256126-183352640 | [ ] 157159612-170256126 | [ ] 144063097-157159611 | [ 1 ] 130966583-144063097 | [ ] 117870068-130966582 | [ ] 104773553-117870067 | [ 1 ] 91677039-104773553 | [ ] 78580524-91677038 | [ 2 ] 65484010-78580524 | [ ] 52387495-65484009 | [ 1 ] 39290980-52387494 | [ ] 26194466-39290980 | [ 3 ] 13097951-26194465 |* [ 7 ] 1437-13097951 |************************************************** [ 198 ] Storage Throughput = good ( 950.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40168764 bp ( 40014775 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:50 (hh:mm:ss) Elapsed Time Round Time: 00:22:35 (hh:mm:ss) Elapsed Time : 127 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3900 repeats masked totaling 1125918 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10086612 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10019117 bp After Masking: 8723893 bp Masked: 12.93 % -- Input Database Coverage: 10086612 bp out of 1053332251 bp ( 0.96 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:10 (hh:mm:ss) Elapsed Time, 29220 HSPs Collected Number of families returned by RECON: 232 Round Time: 00:08:47 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12335 repeats masked totaling 3348143 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30122073 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30035579 bp After Masking: 26059940 bp Masked: 13.24 % -- Input Database Coverage: 40208685 bp out of 1053332251 bp ( 3.82 % ) Sampling Time: 00:03:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:35:22 (hh:mm:ss) Elapsed Time, 5221 HSPs Collected Number of families returned by RECON: 1356 Round Time: 00:39:22 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34260 repeats masked totaling 8849093 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90268405 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90020579 bp After Masking: 79215961 bp Masked: 12.00 % -- Input Database Coverage: 130477090 bp out of 1053332251 bp ( 12.39 % ) Sampling Time: 00:16:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 04:16:29 (hh:mm:ss) Elapsed Time, 48890 HSPs Collected Number of families returned by RECON: 8867 Round Time: 04:39:36 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 110768 repeats masked totaling 29297899 bp(s). - TE Masking time 00:03:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270684103 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 270023761 bp After Masking: 234965139 bp Masked: 12.98 % -- Input Database Coverage: 401161193 bp out of 1053332251 bp ( 38.08 % ) Sampling Time: 00:39:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 31:33:03 (hh:mm:ss) Elapsed Time, 245802 HSPs Collected Number of families returned by RECON: 60410 Round Time: 32:52:31 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatScout/RECON discovery complete: 429 families found Classification Time: 00:30:38 (hh:mm:ss) Elapsed Time Program Time: 39:13:29 (hh:mm:ss) Elapsed Time