RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ggzoNI/RM_742881.SunJun231053492024 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: 1719165227 Database = /dev/shm/rModeler.ggzoNI/GCA_034768055.1_ILVO_Slat_1.0 - Sequences = 251197 - Bases = 328192401 - N50 = 1807 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 71255-76331 | [ 1 ] 66180-71255 | [ ] 61105-66180 | [ ] 56030-61105 | [ ] 50955-56030 | [ ] 45880-50955 | [ ] 40805-45880 | [ 1 ] 35729-40804 | [ ] 30654-35729 | [ ] 25579-30654 | [ 2 ] 20504-25579 | [ 4 ] 15429-20504 | [ 39 ] 10354-15429 | [ 301 ] 5279-10354 | [ 4441 ] 204-5279 |************************************************** [ 246408 ] WARN: The N50 for this assembly is low ( <10,000 ). The de novo methods employed by RepeatModeler are intended for use with long contiguous sequences and may not perform well with an over-abundance of short contigs in the database. Storage Throughput = good ( 812.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40661171 bp ( 40000119 non ambiguous ) - Num Contigs Represented = 31224 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:28 (hh:mm:ss) Elapsed Time Round Time: 00:18:46 (hh:mm:ss) Elapsed Time : 919 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20905 repeats masked totaling 2353899 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10167854 bp Num Contigs Represented = 7952 Non ambiguous bp: Initial: 10001853 bp After Masking: 7457956 bp Masked: 25.43 % -- Input Database Coverage: 10167854 bp out of 328192401 bp ( 3.10 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31613176 Comparison Time: 00:27:53 (hh:mm:ss) Elapsed Time, 18102 HSPs Collected Number of families returned by RECON: 2316 Round Time: 00:29:08 (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 : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65380 repeats masked totaling 7537926 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30495251 bp Num Contigs Represented = 23276 Non ambiguous bp: Initial: 30000118 bp After Masking: 21891835 bp Masked: 27.03 % -- Input Database Coverage: 40663105 bp out of 328192401 bp ( 12.39 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 270874450 Comparison Time: 01:37:33 (hh:mm:ss) Elapsed Time, 78519 HSPs Collected Number of families returned by RECON: 7896 Round Time: 01:42:24 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 213767 repeats masked totaling 25894570 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91455733 bp Num Contigs Represented = 69975 Non ambiguous bp: Initial: 90003428 bp After Masking: 62387413 bp Masked: 30.68 % -- Input Database Coverage: 132118838 bp out of 328192401 bp ( 40.26 % ) Sampling Time: 00:05:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2448215325 Comparison Time: 07:13:29 (hh:mm:ss) Elapsed Time, 390783 HSPs Collected Number of families returned by RECON: 25690 Round Time: 07:39:30 (hh:mm:ss) Elapsed Time : 756 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 530552 repeats masked totaling 68499750 bp(s). - TE Masking time 00:08:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 196073541 bp Num Contigs Represented = 149995 Non ambiguous bp: Initial: 192897990 bp After Masking: 120904206 bp Masked: 37.32 % -- Input Database Coverage: 328192379 bp out of 328192401 bp ( 100.00 % ) Sampling Time: 00:15:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11249325010 Comparison Time: 23:54:24 (hh:mm:ss) Elapsed Time, 639413 HSPs Collected Number of families returned by RECON: 57258 Round Time: 25:41:57 (hh:mm:ss) Elapsed Time : 1025 families discovered. RepeatScout/RECON discovery complete: 2903 families found Classification Time: 01:33:10 (hh:mm:ss) Elapsed Time Program Time: 37:24:56 (hh:mm:ss) Elapsed Time