RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RE5V5o/RM_22960.WedJul170735322024 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: 1721226925 Database = /dev/shm/rModeler.RE5V5o/GCF_013265735.2_USDA_OmykA_1.1 - Sequences = 743 - Bases = 2341688614 - N50 = 81569517 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 96887528-103806877 | [ 4 ] 89968179-96887528 | [ 4 ] 83048830-89968179 | [ 3 ] 76129481-83048830 | [ 3 ] 69210132-76129481 | [ 2 ] 62290783-69210132 | [ 3 ] 55371434-62290783 | [ ] 48452085-55371434 | [ 3 ] 41532736-48452085 | [ 10 ] 34613387-41532736 | [ ] 27694038-34613387 | [ ] 20774689-27694038 | [ ] 13855340-20774689 | [ ] 6935991-13855340 | [ ] 16642-6935991 |************************************************** [ 711 ] Storage Throughput = excellent ( 1038.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40110648 bp ( 40030392 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:39 (hh:mm:ss) Elapsed Time Round Time: 00:40:28 (hh:mm:ss) Elapsed Time : 828 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13513 repeats masked totaling 3529981 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030694 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10028594 bp After Masking: 4020923 bp Masked: 59.91 % -- Input Database Coverage: 10030694 bp out of 2341688614 bp ( 0.43 % ) Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:31:32 (hh:mm:ss) Elapsed Time, 6492 HSPs Collected Number of families returned by RECON: 1056 Round Time: 00:38:58 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43527 repeats masked totaling 11015461 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30079945 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 30001789 bp After Masking: 12856425 bp Masked: 57.15 % -- Input Database Coverage: 40110639 bp out of 2341688614 bp ( 1.71 % ) Sampling Time: 00:15:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:40:28 (hh:mm:ss) Elapsed Time, 53098 HSPs Collected Number of families returned by RECON: 3663 Round Time: 02:00:07 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135126 repeats masked totaling 34244482 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90111931 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 90017324 bp After Masking: 37411379 bp Masked: 58.44 % -- Input Database Coverage: 130222570 bp out of 2341688614 bp ( 5.56 % ) Sampling Time: 00:43:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 04:48:21 (hh:mm:ss) Elapsed Time, 329448 HSPs Collected Number of families returned by RECON: 11291 Round Time: 05:46:32 (hh:mm:ss) Elapsed Time : 451 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:50:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 454680 repeats masked totaling 113285166 bp(s). - TE Masking time 00:10:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270869766 bp Num Contigs Represented = 247 Non ambiguous bp: Initial: 270000812 bp After Masking: 99709531 bp Masked: 63.07 % -- Input Database Coverage: 401092336 bp out of 2341688614 bp ( 17.13 % ) Sampling Time: 02:11:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23239153 Comparison Time: 34:19:03 (hh:mm:ss) Elapsed Time, 998240 HSPs Collected Number of families returned by RECON: 34654 Round Time: 37:32:35 (hh:mm:ss) Elapsed Time : 965 families discovered. RepeatScout/RECON discovery complete: 2372 families found Classification Time: 01:40:04 (hh:mm:ss) Elapsed Time Program Time: 48:18:44 (hh:mm:ss) Elapsed Time