RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1Cd8H2/RM_1099.SatJun291739462024 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: 1719707982 Database = /dev/shm/rModeler.1Cd8H2/GCA_019802505.1_Lin1PacBio.ctg.fa.r3p3_pilon_3_oneline.fasta - Sequences = 2080 - Bases = 699660186 - N50 = 1562179 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 14622697-15667013 | [ 1 ] 13578381-14622696 | [ ] 12534066-13578381 | [ ] 11489750-12534065 | [ 2 ] 10445435-11489750 | [ 1 ] 9401119-10445434 | [ 3 ] 8356804-9401119 | [ 1 ] 7312488-8356803 | [ 1 ] 6268173-7312488 | [ 3 ] 5223857-6268172 | [ 4 ] 4179542-5223857 | [ 9 ] 3135226-4179541 | [ 13 ] 2090911-3135226 | [ 26 ] 1046595-2090910 |** [ 84 ] 2280-1046595 |************************************************** [ 1932 ] Storage Throughput = excellent ( 1013.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006253 bp ( 40006253 non ambiguous ) - Num Contigs Represented = 495 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:46 (hh:mm:ss) Elapsed Time Round Time: 00:26:17 (hh:mm:ss) Elapsed Time : 479 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21534 repeats masked totaling 3296718 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034184 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 10034184 bp After Masking: 5964611 bp Masked: 40.56 % -- Input Database Coverage: 10034184 bp out of 699660186 bp ( 1.43 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37128 Comparison Time: 00:05:40 (hh:mm:ss) Elapsed Time, 4464 HSPs Collected Number of families returned by RECON: 871 Round Time: 00:08:00 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64298 repeats masked totaling 10190619 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011937 bp Num Contigs Represented = 409 Non ambiguous bp: Initial: 30011937 bp After Masking: 17489164 bp Masked: 41.73 % -- Input Database Coverage: 40046121 bp out of 699660186 bp ( 5.72 % ) Sampling Time: 00:06:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 308505 Comparison Time: 00:29:02 (hh:mm:ss) Elapsed Time, 30376 HSPs Collected Number of families returned by RECON: 2882 Round Time: 00:36:38 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 198698 repeats masked totaling 30305523 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007735 bp Num Contigs Represented = 782 Non ambiguous bp: Initial: 90007735 bp After Masking: 52804117 bp Masked: 41.33 % -- Input Database Coverage: 130053856 bp out of 699660186 bp ( 18.59 % ) Sampling Time: 00:18:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2852466 Comparison Time: 03:21:20 (hh:mm:ss) Elapsed Time, 141004 HSPs Collected Number of families returned by RECON: 10468 Round Time: 03:46:09 (hh:mm:ss) Elapsed Time : 284 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 683076 repeats masked totaling 99382038 bp(s). - TE Masking time 00:11:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020453 bp Num Contigs Represented = 1373 Non ambiguous bp: Initial: 270020453 bp After Masking: 149636686 bp Masked: 44.58 % -- Input Database Coverage: 400074309 bp out of 699660186 bp ( 57.18 % ) Sampling Time: 01:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26140065 Comparison Time: 26:14:00 (hh:mm:ss) Elapsed Time, 374115 HSPs Collected Number of families returned by RECON: 38497 Round Time: 28:03:34 (hh:mm:ss) Elapsed Time : 654 families discovered. RepeatScout/RECON discovery complete: 1492 families found Classification Time: 01:05:55 (hh:mm:ss) Elapsed Time Program Time: 34:06:33 (hh:mm:ss) Elapsed Time