RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.e3VrLC/RM_3838415.MonJul81021122024 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: 1720459271 Database = /dev/shm/rModeler.e3VrLC/GCF_030506205.1_PD_contigs_1.0 - Sequences = 610 - Bases = 1425974144 - N50 = 14380121 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 42749971-45803368 | [ 1 ] 39696574-42749970 | [ ] 36643177-39696573 | [ ] 33589780-36643176 | [ ] 30536383-33589779 | [ 3 ] 27482986-30536382 | [ 2 ] 24429589-27482985 | [ 4 ] 21376193-24429589 | [ 1 ] 18322796-21376192 |* [ 10 ] 15269399-18322795 | [ 6 ] 12216002-15269398 |* [ 13 ] 9162605-12216001 |* [ 16 ] 6109208-9162604 |* [ 17 ] 3055811-6109207 |*** [ 37 ] 2415-3055811 |************************************************** [ 500 ] Storage Throughput = excellent ( 1501.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010399 bp ( 40010399 non ambiguous ) - Num Contigs Represented = 177 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:38 (hh:mm:ss) Elapsed Time Round Time: 00:23:49 (hh:mm:ss) Elapsed Time : 1206 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18916 repeats masked totaling 4222587 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023517 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 10023517 bp After Masking: 5250738 bp Masked: 47.62 % -- Input Database Coverage: 10023517 bp out of 1425974144 bp ( 0.70 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 13175 HSPs Collected Number of families returned by RECON: 1344 Round Time: 00:06:31 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56276 repeats masked totaling 13041291 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026882 bp Num Contigs Represented = 159 Non ambiguous bp: Initial: 30026882 bp After Masking: 15047543 bp Masked: 49.89 % -- Input Database Coverage: 40050399 bp out of 1425974144 bp ( 2.81 % ) Sampling Time: 00:03:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:21:37 (hh:mm:ss) Elapsed Time, 47098 HSPs Collected Number of families returned by RECON: 4022 Round Time: 00:26:36 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177865 repeats masked totaling 39380507 bp(s). - TE Masking time 00:03:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032768 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 90032768 bp After Masking: 45222314 bp Masked: 49.77 % -- Input Database Coverage: 130083167 bp out of 1425974144 bp ( 9.12 % ) Sampling Time: 00:10:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:11:32 (hh:mm:ss) Elapsed Time, 350705 HSPs Collected Number of families returned by RECON: 11450 Round Time: 02:32:08 (hh:mm:ss) Elapsed Time : 641 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 596420 repeats masked totaling 136501610 bp(s). - TE Masking time 00:17:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011959 bp Num Contigs Represented = 316 Non ambiguous bp: Initial: 270011959 bp After Masking: 116263547 bp Masked: 56.94 % -- Input Database Coverage: 400095126 bp out of 1425974144 bp ( 28.06 % ) Sampling Time: 00:40:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 15:05:25 (hh:mm:ss) Elapsed Time, 1007220 HSPs Collected Number of families returned by RECON: 32191 Round Time: 16:31:40 (hh:mm:ss) Elapsed Time : 1232 families discovered. RepeatScout/RECON discovery complete: 3191 families found Classification Time: 02:22:26 (hh:mm:ss) Elapsed Time Program Time: 22:23:10 (hh:mm:ss) Elapsed Time