RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KXn64T/RM_1718385.WedMar131844022024 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: 1710380642 Database = /dev/shm/rModeler.KXn64T/GCA_035084215.1_sHepPer1.hap1 - Sequences = 1880 - Bases = 3249935392 - N50 = 73985925 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 185325645-198562713 | [ 1 ] 172088577-185325644 | [ 1 ] 158851509-172088576 | [ ] 145614441-158851508 | [ ] 132377373-145614440 | [ 3 ] 119140305-132377372 | [ ] 105903237-119140304 | [ 1 ] 92666169-105903236 | [ 1 ] 79429101-92666168 | [ 4 ] 66192033-79429100 | [ 5 ] 52954965-66192032 | [ 5 ] 39717897-52954964 | [ 7 ] 26480829-39717896 | [ 9 ] 13243761-26480828 | [ 6 ] 6694-13243761 |************************************************** [ 1837 ] Storage Throughput = excellent ( 1249.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036880 bp ( 40032273 non ambiguous ) - Num Contigs Represented = 174 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:17 (hh:mm:ss) Elapsed Time Round Time: 00:26:05 (hh:mm:ss) Elapsed Time : 379 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13571 repeats masked totaling 4644396 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000867 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 10000267 bp After Masking: 3890408 bp Masked: 61.10 % -- Input Database Coverage: 10000867 bp out of 3249935392 bp ( 0.31 % ) Sampling Time: 00:05:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:16 (hh:mm:ss) Elapsed Time, 7915 HSPs Collected Number of families returned by RECON: 988 Round Time: 00:09:56 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42251 repeats masked totaling 13916667 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035996 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 30031989 bp After Masking: 11149952 bp Masked: 62.87 % -- Input Database Coverage: 40036863 bp out of 3249935392 bp ( 1.23 % ) Sampling Time: 00:17:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:18:36 (hh:mm:ss) Elapsed Time, 35192 HSPs Collected Number of families returned by RECON: 3025 Round Time: 00:38:59 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:57:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136315 repeats masked totaling 44162701 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032058 bp Num Contigs Represented = 260 Non ambiguous bp: Initial: 90022058 bp After Masking: 30309924 bp Masked: 66.33 % -- Input Database Coverage: 130068921 bp out of 3249935392 bp ( 4.00 % ) Sampling Time: 01:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:44:49 (hh:mm:ss) Elapsed Time, 138044 HSPs Collected Number of families returned by RECON: 7944 Round Time: 02:51:55 (hh:mm:ss) Elapsed Time : 268 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:30:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465115 repeats masked totaling 141426559 bp(s). - TE Masking time 00:06:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039167 bp Num Contigs Represented = 523 Non ambiguous bp: Initial: 270012297 bp After Masking: 82551616 bp Masked: 69.43 % -- Input Database Coverage: 400108088 bp out of 3249935392 bp ( 12.31 % ) Sampling Time: 02:48:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23245971 Comparison Time: 10:29:52 (hh:mm:ss) Elapsed Time, 373559 HSPs Collected Number of families returned by RECON: 22380 Round Time: 13:38:35 (hh:mm:ss) Elapsed Time : 755 families discovered. RepeatScout/RECON discovery complete: 1512 families found Classification Time: 00:59:13 (hh:mm:ss) Elapsed Time Program Time: 18:44:43 (hh:mm:ss) Elapsed Time