RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.adMNbV/RM_28603.WedJan111125172023 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: 1673465116 Database = /dev/shm/rModeler.adMNbV/GCA_017639485.1_bPluApr1.pri - Sequences = 107 - Bases = 1247767512 - N50 = 130366996 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207844435-222690203 | [ 1 ] 192998667-207844434 | [ ] 178152900-192998667 | [ ] 163307132-178152899 | [ 1 ] 148461364-163307131 | [ ] 133615597-148461364 | [ ] 118769829-133615596 | [ 1 ] 103924061-118769828 | [ ] 89078294-103924061 | [ ] 74232526-89078293 |* [ 3 ] 59386758-74232525 | [ 1 ] 44540991-59386758 | [ ] 29695223-44540990 |* [ 3 ] 14849455-29695222 |***** [ 9 ] 3688-14849455 |************************************************** [ 88 ] Storage Throughput = excellent ( 1082.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40268218 bp ( 40002603 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:34 (hh:mm:ss) Elapsed Time Round Time: 00:27:36 (hh:mm:ss) Elapsed Time : 38 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1406 repeats masked totaling 725966 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082882 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10002778 bp After Masking: 9232119 bp Masked: 7.70 % -- Input Database Coverage: 10082882 bp out of 1247767512 bp ( 0.81 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:25 (hh:mm:ss) Elapsed Time, 445 HSPs Collected Number of families returned by RECON: 222 Round Time: 00:08:23 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4378 repeats masked totaling 2219392 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30225257 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30039746 bp After Masking: 27712198 bp Masked: 7.75 % -- Input Database Coverage: 40308139 bp out of 1247767512 bp ( 3.23 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:39:39 (hh:mm:ss) Elapsed Time, 5570 HSPs Collected Number of families returned by RECON: 1466 Round Time: 00:43:02 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15814 repeats masked totaling 7022393 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91061690 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90009559 bp After Masking: 82599375 bp Masked: 8.23 % -- Input Database Coverage: 131369829 bp out of 1247767512 bp ( 10.53 % ) Sampling Time: 00:08:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 04:46:31 (hh:mm:ss) Elapsed Time, 29024 HSPs Collected Number of families returned by RECON: 8207 Round Time: 04:56:54 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55154 repeats masked totaling 23717313 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273007997 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270037139 bp After Masking: 245058696 bp Masked: 9.25 % -- Input Database Coverage: 404377826 bp out of 1247767512 bp ( 32.41 % ) Sampling Time: 00:25:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23416746 Comparison Time: 38:39:16 (hh:mm:ss) Elapsed Time, 163753 HSPs Collected Number of families returned by RECON: 53772 Round Time: 39:53:15 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatScout/RECON discovery complete: 325 families found Classification Time: 00:20:44 (hh:mm:ss) Elapsed Time Program Time: 46:29:54 (hh:mm:ss) Elapsed Time