RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GTmgJl/RM_3089844.ThuJun271242222024 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: 1719517342 Database = /dev/shm/rModeler.GTmgJl/GCF_035770615.1_bMelMel2.pri - Sequences = 353 - Bases = 1541245192 - N50 = 82773674 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 163214180-174870981 | [ 1 ] 151557379-163214179 | [ ] 139900578-151557378 | [ 2 ] 128243777-139900577 | [ ] 116586976-128243776 | [ ] 104930175-116586975 | [ ] 93273374-104930174 | [ 2 ] 81616574-93273374 | [ 1 ] 69959773-81616573 | [ 1 ] 58302972-69959772 | [ 1 ] 46646171-58302971 | [ ] 34989370-46646170 | [ 2 ] 23332569-34989369 | [ 4 ] 11675768-23332568 |** [ 16 ] 18968-11675768 |************************************************** [ 323 ] Storage Throughput = excellent ( 1204.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027150 bp ( 40003216 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:03 (hh:mm:ss) Elapsed Time Round Time: 00:31:29 (hh:mm:ss) Elapsed Time : 246 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 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3778 repeats masked totaling 1653899 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017495 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10003942 bp After Masking: 6793200 bp Masked: 32.09 % -- Input Database Coverage: 10017495 bp out of 1541245192 bp ( 0.65 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 2985 HSPs Collected Number of families returned by RECON: 282 Round Time: 00:07:07 (hh:mm:ss) Elapsed Time : 6 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 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12587 repeats masked totaling 5882415 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30049655 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30039274 bp After Masking: 19848210 bp Masked: 33.93 % -- Input Database Coverage: 40067150 bp out of 1541245192 bp ( 2.60 % ) Sampling Time: 00:05:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:24:42 (hh:mm:ss) Elapsed Time, 15378 HSPs Collected Number of families returned by RECON: 1297 Round Time: 00:32:03 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41397 repeats masked totaling 18752282 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023813 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 90001463 bp After Masking: 58600166 bp Masked: 34.89 % -- Input Database Coverage: 130090963 bp out of 1541245192 bp ( 8.44 % ) Sampling Time: 00:20:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:48:30 (hh:mm:ss) Elapsed Time, 67092 HSPs Collected Number of families returned by RECON: 7189 Round Time: 03:11:27 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136891 repeats masked totaling 60717389 bp(s). - TE Masking time 00:07:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270212308 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 270033969 bp After Masking: 173867114 bp Masked: 35.61 % -- Input Database Coverage: 400303271 bp out of 1541245192 bp ( 25.97 % ) Sampling Time: 00:49:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 20:52:07 (hh:mm:ss) Elapsed Time, 319751 HSPs Collected Number of families returned by RECON: 46439 Round Time: 22:13:21 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatScout/RECON discovery complete: 719 families found Classification Time: 00:57:26 (hh:mm:ss) Elapsed Time Program Time: 27:32:53 (hh:mm:ss) Elapsed Time