RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nSrc93/RM_2561110.FriMar150852492024 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: 1710517969 Database = /dev/shm/rModeler.nSrc93/GCA_035770615.1_bMelMel2.pri - Sequences = 354 - Bases = 1541261971 - N50 = 82773674 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 163214034-174870981 | [ 1 ] 151557087-163214033 | [ ] 139900140-151557086 | [ 2 ] 128243193-139900139 | [ ] 116586247-128243193 | [ ] 104929300-116586246 | [ ] 93272353-104929299 | [ 2 ] 81615406-93272352 | [ 1 ] 69958459-81615405 | [ 1 ] 58301513-69958459 | [ 1 ] 46644566-58301512 | [ ] 34987619-46644565 | [ 2 ] 23330672-34987618 | [ 4 ] 11673725-23330671 |** [ 16 ] 16779-11673725 |************************************************** [ 324 ] Storage Throughput = excellent ( 1322.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028793 bp ( 40028380 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:33 (hh:mm:ss) Elapsed Time Round Time: 00:31:04 (hh:mm:ss) Elapsed Time : 256 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3974 repeats masked totaling 1739150 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027265 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10027265 bp After Masking: 6840189 bp Masked: 31.78 % -- Input Database Coverage: 10027265 bp out of 1541261971 bp ( 0.65 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 1494 HSPs Collected Number of families returned by RECON: 241 Round Time: 00:07:57 (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 : 00:01:07 (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... 12288 repeats masked totaling 6626729 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001448 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 30001035 bp After Masking: 19047577 bp Masked: 36.51 % -- Input Database Coverage: 40028713 bp out of 1541261971 bp ( 2.60 % ) Sampling Time: 00:06:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:40 (hh:mm:ss) Elapsed Time, 9135 HSPs Collected Number of families returned by RECON: 1164 Round Time: 00:33:00 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36495 repeats masked totaling 18121023 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90078686 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 90030162 bp After Masking: 59619414 bp Masked: 33.78 % -- Input Database Coverage: 130107399 bp out of 1541261971 bp ( 8.44 % ) Sampling Time: 00:16:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:47:34 (hh:mm:ss) Elapsed Time, 66727 HSPs Collected Number of families returned by RECON: 7503 Round Time: 03:07:34 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118789 repeats masked totaling 58870602 bp(s). - TE Masking time 00:07:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270239451 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 270026711 bp After Masking: 173685649 bp Masked: 35.68 % -- Input Database Coverage: 400346850 bp out of 1541261971 bp ( 25.98 % ) Sampling Time: 00:51:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 20:04:04 (hh:mm:ss) Elapsed Time, 223155 HSPs Collected Number of families returned by RECON: 46223 Round Time: 21:23:31 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatScout/RECON discovery complete: 697 families found Classification Time: 01:03:59 (hh:mm:ss) Elapsed Time Program Time: 26:47:05 (hh:mm:ss) Elapsed Time