RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.VVN9wB/RM_1457837.MonNov182108252024 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: 1731992905 Database = /scratch/tmp/rModeler.VVN9wB/GCA_964106915.2_rPodGai1.hap1.2 - Sequences = 211 - Bases = 1514643635 - N50 = 99788972 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 129595766-138852535 | [ 1 ] 120338997-129595766 | [ 2 ] 111082228-120338997 | [ ] 101825459-111082228 | [ 1 ] 92568690-101825459 | [ 2 ] 83311921-92568690 | [ 2 ] 74055152-83311921 | [ 2 ] 64798383-74055152 | [ 1 ] 55541614-64798383 | [ 2 ] 46284845-55541614 | [ 3 ] 37028076-46284845 | [ 2 ] 27771307-37028076 | [ 1 ] 18514538-27771307 | [ ] 9257769-18514538 | [ 1 ] 1000-9257769 |************************************************** [ 191 ] Storage Throughput = excellent ( 1473.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015266 bp ( 40010248 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:08 (hh:mm:ss) Elapsed Time Round Time: 00:11:36 (hh:mm:ss) Elapsed Time : 536 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17504 repeats masked totaling 3237196 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003580 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10002362 bp After Masking: 6535288 bp Masked: 34.66 % -- Input Database Coverage: 10003580 bp out of 1514643635 bp ( 0.66 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:01 (hh:mm:ss) Elapsed Time, 12332 HSPs Collected Number of families returned by RECON: 1288 Round Time: 00:03:40 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53433 repeats masked totaling 9915303 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011675 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30007875 bp After Masking: 18863144 bp Masked: 37.14 % -- Input Database Coverage: 40015255 bp out of 1514643635 bp ( 2.64 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:07 (hh:mm:ss) Elapsed Time, 43859 HSPs Collected Number of families returned by RECON: 4228 Round Time: 00:14:41 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177050 repeats masked totaling 32054782 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028359 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90019759 bp After Masking: 54891186 bp Masked: 39.02 % -- Input Database Coverage: 130043614 bp out of 1514643635 bp ( 8.59 % ) Sampling Time: 00:04:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:05:31 (hh:mm:ss) Elapsed Time, 213035 HSPs Collected Number of families returned by RECON: 13857 Round Time: 01:14:25 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 591611 repeats masked totaling 106413647 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038168 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 270005368 bp After Masking: 154595981 bp Masked: 42.74 % -- Input Database Coverage: 400081782 bp out of 1514643635 bp ( 26.41 % ) Sampling Time: 00:14:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 07:42:43 (hh:mm:ss) Elapsed Time, 808399 HSPs Collected Number of families returned by RECON: 47910 Round Time: 08:24:06 (hh:mm:ss) Elapsed Time : 1048 families discovered. RepeatScout/RECON discovery complete: 2171 families found Classification Time: 00:31:50 (hh:mm:ss) Elapsed Time Program Time: 10:40:18 (hh:mm:ss) Elapsed Time