RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DFPVCK/RM_25863.SatNov252138152023 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: 1700977094 Database = /dev/shm/rModeler.DFPVCK/GCA_023637925.1_DD_ASM_B1a - Sequences = 230 - Bases = 1014956223 - N50 = 19019515 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52870213-56646400 | [ 2 ] 49094026-52870212 | [ 1 ] 45317839-49094025 | [ ] 41541653-45317839 | [ ] 37765466-41541652 | [ 1 ] 33989279-37765465 | [ 2 ] 30213092-33989278 | [ ] 26436906-30213092 | [ ] 22660719-26436905 |* [ 4 ] 18884532-22660718 |** [ 7 ] 15108345-18884531 |* [ 6 ] 11332159-15108345 |** [ 9 ] 7555972-11332158 |*** [ 13 ] 3779785-7555971 |** [ 10 ] 3599-3779785 |************************************************** [ 175 ] Storage Throughput = excellent ( 1212.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014321 bp ( 40014321 non ambiguous ) - Num Contigs Represented = 108 - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:02 (hh:mm:ss) Elapsed Time Round Time: 00:26:37 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (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... 1949 repeats masked totaling 555845 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000384 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 10000384 bp After Masking: 9342351 bp Masked: 6.58 % -- Input Database Coverage: 10000384 bp out of 1014956223 bp ( 0.99 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:40 (hh:mm:ss) Elapsed Time, 494 HSPs Collected Number of families returned by RECON: 293 Round Time: 00:08:16 (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 : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5846 repeats masked totaling 1618067 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013927 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30013927 bp After Masking: 28111465 bp Masked: 6.34 % -- Input Database Coverage: 40014311 bp out of 1014956223 bp ( 3.94 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:44:41 (hh:mm:ss) Elapsed Time, 6065 HSPs Collected Number of families returned by RECON: 1741 Round Time: 00:47:26 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19052 repeats masked totaling 5393400 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026847 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 90026847 bp After Masking: 83923635 bp Masked: 6.78 % -- Input Database Coverage: 130041158 bp out of 1014956223 bp ( 12.81 % ) Sampling Time: 00:04:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 05:48:35 (hh:mm:ss) Elapsed Time, 35705 HSPs Collected Number of families returned by RECON: 11858 Round Time: 05:56:06 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63071 repeats masked totaling 17857297 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015490 bp Num Contigs Represented = 173 Non ambiguous bp: Initial: 270015490 bp After Masking: 249819292 bp Masked: 7.48 % -- Input Database Coverage: 400056648 bp out of 1014956223 bp ( 39.42 % ) Sampling Time: 00:14:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 48:02:56 (hh:mm:ss) Elapsed Time, 202185 HSPs Collected Number of families returned by RECON: 81033 Round Time: 49:41:58 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatScout/RECON discovery complete: 257 families found Classification Time: 00:12:57 (hh:mm:ss) Elapsed Time Program Time: 57:13:20 (hh:mm:ss) Elapsed Time