RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.cUx0FY/RM_10554.SunDec30427532023 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: 1701606472 Database = /dev/shm/rModeler.cUx0FY/GCA_030463565.1_bPelCri1.pri - Sequences = 311 - Bases = 1314587946 - N50 = 133472355 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 212734068-227928177 | [ 1 ] 197539959-212734068 | [ ] 182345850-197539959 | [ ] 167151741-182345850 | [ 1 ] 151957632-167151741 | [ ] 136763523-151957632 | [ ] 121569414-136763523 | [ 1 ] 106375305-121569414 | [ ] 91181196-106375305 | [ ] 75987087-91181196 | [ 3 ] 60792978-75987087 | [ 1 ] 45598869-60792978 | [ 2 ] 30404760-45598869 | [ 3 ] 15210651-30404760 | [ 4 ] 16542-15210651 |************************************************** [ 295 ] Storage Throughput = excellent ( 1228.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018646 bp ( 40015446 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:52 (hh:mm:ss) Elapsed Time Round Time: 00:32:12 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1890 repeats masked totaling 793090 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017181 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10015981 bp After Masking: 8983548 bp Masked: 10.31 % -- Input Database Coverage: 10017181 bp out of 1314587946 bp ( 0.76 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:22 (hh:mm:ss) Elapsed Time, 2301 HSPs Collected Number of families returned by RECON: 308 Round Time: 00:07:35 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6885 repeats masked totaling 2722209 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041460 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30039460 bp After Masking: 26165641 bp Masked: 12.90 % -- Input Database Coverage: 40058641 bp out of 1314587946 bp ( 3.05 % ) Sampling Time: 00:14:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:42:43 (hh:mm:ss) Elapsed Time, 88568 HSPs Collected Number of families returned by RECON: 1507 Round Time: 00:58:20 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19982 repeats masked totaling 7637886 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010111 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 90005543 bp After Masking: 78890766 bp Masked: 12.35 % -- Input Database Coverage: 130068752 bp out of 1314587946 bp ( 9.89 % ) Sampling Time: 00:10:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 04:46:41 (hh:mm:ss) Elapsed Time, 1121057 HSPs Collected Number of families returned by RECON: 8578 Round Time: 05:07:11 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69198 repeats masked totaling 25394992 bp(s). - TE Masking time 00:03:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270024643 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 270009748 bp After Masking: 234347798 bp Masked: 13.21 % -- Input Database Coverage: 400093395 bp out of 1314587946 bp ( 30.43 % ) Sampling Time: 00:32:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 37:59:49 (hh:mm:ss) Elapsed Time, 5419748 HSPs Collected Number of families returned by RECON: 54748 Round Time: 39:34:31 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatScout/RECON discovery complete: 333 families found Classification Time: 00:33:20 (hh:mm:ss) Elapsed Time Program Time: 46:53:09 (hh:mm:ss) Elapsed Time