RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hZVDEu/RM_29584.ThuNov300949052023 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: 1701366544 Database = /dev/shm/rModeler.hZVDEu/GCA_029633875.1_fHopMal1.hap2 - Sequences = 452 - Bases = 1117251445 - N50 = 55498077 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 84972061-91041448 | [ 3 ] 78902675-84972061 | [ 1 ] 72833288-78902674 | [ 1 ] 66763902-72833288 | [ ] 60694516-66763902 | [ 1 ] 54625129-60694515 | [ 1 ] 48555743-54625129 | [ 1 ] 42486356-48555742 | [ 4 ] 36416970-42486356 | [ 5 ] 30347584-36416970 | [ 2 ] 24278197-30347583 | [ ] 18208811-24278197 | [ ] 12139424-18208810 | [ ] 6070038-12139424 | [ ] 652-6070038 |************************************************** [ 433 ] Storage Throughput = excellent ( 1063.24 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41789504 bp ( 40006510 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:29:31 (hh:mm:ss) Elapsed Time Round Time: 00:41:10 (hh:mm:ss) Elapsed Time : 559 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14210 repeats masked totaling 2722683 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10712808 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10039322 bp After Masking: 6016096 bp Masked: 40.07 % -- Input Database Coverage: 10712808 bp out of 1117251445 bp ( 0.96 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36315 Comparison Time: 00:06:24 (hh:mm:ss) Elapsed Time, 7418 HSPs Collected Number of families returned by RECON: 1254 Round Time: 00:08:51 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43426 repeats masked totaling 7858357 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31116692 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30007184 bp After Masking: 18960194 bp Masked: 36.81 % -- Input Database Coverage: 41829500 bp out of 1117251445 bp ( 3.74 % ) Sampling Time: 00:06:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 306153 Comparison Time: 00:32:24 (hh:mm:ss) Elapsed Time, 191329 HSPs Collected Number of families returned by RECON: 4882 Round Time: 00:41:10 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 146595 repeats masked totaling 25436820 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 94295720 bp Num Contigs Represented = 123 Non ambiguous bp: Initial: 90034812 bp After Masking: 54472532 bp Masked: 39.50 % -- Input Database Coverage: 136125220 bp out of 1117251445 bp ( 12.18 % ) Sampling Time: 00:19:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2821500 Comparison Time: 03:32:23 (hh:mm:ss) Elapsed Time, 934127 HSPs Collected Number of families returned by RECON: 14735 Round Time: 06:35:46 (hh:mm:ss) Elapsed Time : 450 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 510344 repeats masked totaling 91404335 bp(s). - TE Masking time 00:13:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 281288199 bp Num Contigs Represented = 228 Non ambiguous bp: Initial: 270002753 bp After Masking: 150002721 bp Masked: 44.44 % -- Input Database Coverage: 417413419 bp out of 1117251445 bp ( 37.36 % ) Sampling Time: 01:05:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25102155 Comparison Time: 25:47:49 (hh:mm:ss) Elapsed Time, 962893 HSPs Collected Number of families returned by RECON: 48881 Round Time: 28:11:18 (hh:mm:ss) Elapsed Time : 998 families discovered. RepeatScout/RECON discovery complete: 2141 families found Classification Time: 01:50:04 (hh:mm:ss) Elapsed Time Program Time: 38:08:19 (hh:mm:ss) Elapsed Time