RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TfIRxQ/RM_17434.SatJan141912232023 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: 1673752342 Database = /dev/shm/rModeler.TfIRxQ/GCF_903992535.2_mArvAmp1.2 - Sequences = 215 - Bases = 2297766297 - N50 = 160717644 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 187160832-200529155 | [ 3 ] 173792509-187160831 | [ ] 160424186-173792508 | [ 3 ] 147055864-160424186 | [ 1 ] 133687541-147055863 | [ 2 ] 120319218-133687540 |* [ 4 ] 106950895-120319217 | [ ] 93582573-106950895 | [ ] 80214250-93582572 | [ ] 66845927-80214249 | [ 1 ] 53477604-66845926 | [ 2 ] 40109282-53477604 | [ 1 ] 26740959-40109281 | [ 1 ] 13372636-26740958 | [ ] 4314-13372636 |************************************************** [ 197 ] Storage Throughput = excellent ( 1152.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40220328 bp ( 40036319 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:03:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:14 (hh:mm:ss) Elapsed Time Round Time: 00:28:20 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14966 repeats masked totaling 2577036 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10094530 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10032545 bp After Masking: 7279834 bp Masked: 27.44 % -- Input Database Coverage: 10094530 bp out of 2297766297 bp ( 0.44 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:38 (hh:mm:ss) Elapsed Time, 7397 HSPs Collected Number of families returned by RECON: 785 Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45895 repeats masked totaling 8211973 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30125718 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30003694 bp After Masking: 21115085 bp Masked: 29.63 % -- Input Database Coverage: 40220248 bp out of 2297766297 bp ( 1.75 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:31:35 (hh:mm:ss) Elapsed Time, 19111 HSPs Collected Number of families returned by RECON: 2273 Round Time: 00:37:05 (hh:mm:ss) Elapsed Time : 49 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153443 repeats masked totaling 27335156 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90258114 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90006260 bp After Masking: 60874898 bp Masked: 32.37 % -- Input Database Coverage: 130478362 bp out of 2297766297 bp ( 5.68 % ) Sampling Time: 00:12:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:27:18 (hh:mm:ss) Elapsed Time, 93315 HSPs Collected Number of families returned by RECON: 8607 Round Time: 03:43:52 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 491306 repeats masked totaling 87697372 bp(s). - TE Masking time 00:06:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270558416 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 270008486 bp After Masking: 177175952 bp Masked: 34.38 % -- Input Database Coverage: 401036778 bp out of 2297766297 bp ( 17.45 % ) Sampling Time: 00:37:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 26:17:19 (hh:mm:ss) Elapsed Time, 212010 HSPs Collected Number of families returned by RECON: 37518 Round Time: 27:26:27 (hh:mm:ss) Elapsed Time : 379 families discovered. RepeatScout/RECON discovery complete: 901 families found Classification Time: 00:32:56 (hh:mm:ss) Elapsed Time Program Time: 32:57:05 (hh:mm:ss) Elapsed Time