RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.fCUvRu/RM_10908.SunDec80553202024 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: 1733665999 Database = /scratch/tmp/rModeler.fCUvRu/GCA_038363225.1_mArtInt1.hap2 - Sequences = 187 - Bases = 2080478059 - N50 = 178263551 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 228405638-244719554 | [ 1 ] 212091723-228405638 | [ 1 ] 195777808-212091723 | [ 1 ] 179463893-195777808 | [ 1 ] 163149978-179463893 | [ 2 ] 146836062-163149977 | [ 1 ] 130522147-146836062 | [ 2 ] 114208232-130522147 | [ 1 ] 97894317-114208232 | [ 2 ] 81580402-97894317 | [ ] 65266486-81580401 | [ ] 48952571-65266486 | [ 2 ] 32638656-48952571 | [ ] 16324741-32638656 | [ ] 10826-16324741 |************************************************** [ 173 ] Storage Throughput = fair ( 615.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021674 bp ( 40021374 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:03:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:45 (hh:mm:ss) Elapsed Time Round Time: 00:36:56 (hh:mm:ss) Elapsed Time : 209 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:52 (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... 7427 repeats masked totaling 2298336 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000263 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10000263 bp After Masking: 7607480 bp Masked: 23.93 % -- Input Database Coverage: 10000263 bp out of 2080478059 bp ( 0.48 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:10 (hh:mm:ss) Elapsed Time, 39130 HSPs Collected Number of families returned by RECON: 773 Round Time: 00:07:53 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26134 repeats masked totaling 7363429 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021408 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30021108 bp After Masking: 22230070 bp Masked: 25.95 % -- Input Database Coverage: 40021671 bp out of 2080478059 bp ( 1.92 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:33:29 (hh:mm:ss) Elapsed Time, 308839 HSPs Collected Number of families returned by RECON: 2423 Round Time: 00:38:41 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85929 repeats masked totaling 23955156 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019824 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 90019424 bp After Masking: 64929010 bp Masked: 27.87 % -- Input Database Coverage: 130041495 bp out of 2080478059 bp ( 6.25 % ) Sampling Time: 00:12:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 04:04:41 (hh:mm:ss) Elapsed Time, 2792596 HSPs Collected Number of families returned by RECON: 8289 Round Time: 04:25:01 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 303210 repeats masked totaling 81726117 bp(s). - TE Masking time 00:06:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017977 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 270016977 bp After Masking: 185333811 bp Masked: 31.36 % -- Input Database Coverage: 400059472 bp out of 2080478059 bp ( 19.23 % ) Sampling Time: 00:40:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 30:07:58 (hh:mm:ss) Elapsed Time, 20608378 HSPs Collected Number of families returned by RECON: 36775 Round Time: 31:38:59 (hh:mm:ss) Elapsed Time : 360 families discovered. RepeatScout/RECON discovery complete: 838 families found Classification Time: 00:39:16 (hh:mm:ss) Elapsed Time Program Time: 38:06:46 (hh:mm:ss) Elapsed Time