RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jmNE1w/RM_307010.FriJan121246352024 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: 1705092389 Database = /dev/shm/rModeler.jmNE1w/GCF_028564815.1_mEubGla1.1.hap2._XY - Sequences = 789 - Bases = 2843691573 - N50 = 133752502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 224782628-240837649 | [ 1 ] 208727607-224782627 | [ ] 192672587-208727607 | [ 2 ] 176617566-192672586 | [ 1 ] 160562545-176617565 | [ ] 144507525-160562545 | [ 2 ] 128452504-144507524 | [ 3 ] 112397483-128452503 | [ 3 ] 96342463-112397483 | [ 1 ] 80287442-96342462 | [ 5 ] 64232421-80287441 | [ 1 ] 48177401-64232421 | [ 2 ] 32122380-48177400 | [ ] 16067359-32122379 | [ ] 12339-16067359 |************************************************** [ 768 ] Storage Throughput = excellent ( 1193.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40078163 bp ( 40038354 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:16 (hh:mm:ss) Elapsed Time Round Time: 00:31:30 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8623 repeats masked totaling 2885922 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027801 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10027401 bp After Masking: 6983269 bp Masked: 30.36 % -- Input Database Coverage: 10027801 bp out of 2843691573 bp ( 0.35 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:29:43 (hh:mm:ss) Elapsed Time, 142132 HSPs Collected Number of families returned by RECON: 836 Round Time: 00:34:49 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30844 repeats masked totaling 10463212 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30050361 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30010952 bp After Masking: 18730397 bp Masked: 37.59 % -- Input Database Coverage: 40078162 bp out of 2843691573 bp ( 1.41 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:23:29 (hh:mm:ss) Elapsed Time, 355760 HSPs Collected Number of families returned by RECON: 2102 Round Time: 01:38:34 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101388 repeats masked totaling 34187110 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90262830 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 90012353 bp After Masking: 53088141 bp Masked: 41.02 % -- Input Database Coverage: 130340992 bp out of 2843691573 bp ( 4.58 % ) Sampling Time: 00:11:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 03:17:48 (hh:mm:ss) Elapsed Time, 109350 HSPs Collected Number of families returned by RECON: 8118 Round Time: 03:34:29 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 350452 repeats masked totaling 113346734 bp(s). - TE Masking time 00:02:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270491530 bp Num Contigs Represented = 284 Non ambiguous bp: Initial: 270024151 bp After Masking: 148966385 bp Masked: 44.83 % -- Input Database Coverage: 400832522 bp out of 2843691573 bp ( 14.10 % ) Sampling Time: 00:31:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 14:32:02 (hh:mm:ss) Elapsed Time, 431894 HSPs Collected Number of families returned by RECON: 30361 Round Time: 15:21:23 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatScout/RECON discovery complete: 781 families found Classification Time: 00:21:19 (hh:mm:ss) Elapsed Time Program Time: 22:02:04 (hh:mm:ss) Elapsed Time