RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.oOpAyZ/RM_745126.FriMay120958592023 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: 1683910739 Database = /dev/shm/rModeler.oOpAyZ/GCA_028022735.1_bGypBar2.pri - Sequences = 232 - Bases = 1365299843 - N50 = 53105323 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 85442906-91544569 | [ 2 ] 79341244-85442906 | [ 2 ] 73239582-79341244 | [ 1 ] 67137919-73239581 | [ 2 ] 61036257-67137919 | [ ] 54934595-61036257 | [ 1 ] 48832933-54934595 |* [ 5 ] 42731270-48832932 | [ 3 ] 36629608-42731270 | [ 2 ] 30527946-36629608 | [ 3 ] 24426284-30527946 | [ 3 ] 18324621-24426283 | [ 3 ] 12222959-18324621 | [ ] 6121297-12222959 | [ ] 19635-6121297 |************************************************** [ 205 ] Storage Throughput = excellent ( 1383.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044266 bp ( 40002229 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:28 (hh:mm:ss) Elapsed Time Round Time: 00:20:41 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1162 repeats masked totaling 467516 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023600 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10023600 bp After Masking: 8757170 bp Masked: 12.63 % -- Input Database Coverage: 10023600 bp out of 1365299843 bp ( 0.73 % ) Sampling Time: 00:01:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:08:25 (hh:mm:ss) Elapsed Time, 9941 HSPs Collected Number of families returned by RECON: 292 Round Time: 00:11:16 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3956 repeats masked totaling 1870637 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30060660 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30018623 bp After Masking: 24778017 bp Masked: 17.46 % -- Input Database Coverage: 40084260 bp out of 1365299843 bp ( 2.94 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:36:13 (hh:mm:ss) Elapsed Time, 9893 HSPs Collected Number of families returned by RECON: 1493 Round Time: 00:41:10 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12267 repeats masked totaling 5583358 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90152848 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90004815 bp After Masking: 76568300 bp Masked: 14.93 % -- Input Database Coverage: 130237108 bp out of 1365299843 bp ( 9.54 % ) Sampling Time: 00:10:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:58:36 (hh:mm:ss) Elapsed Time, 44066 HSPs Collected Number of families returned by RECON: 8910 Round Time: 04:12:28 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52117 repeats masked totaling 20688992 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270589685 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270010487 bp After Masking: 226074917 bp Masked: 16.27 % -- Input Database Coverage: 400826793 bp out of 1365299843 bp ( 29.36 % ) Sampling Time: 00:32:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 30:26:10 (hh:mm:ss) Elapsed Time, 185786 HSPs Collected Number of families returned by RECON: 53904 Round Time: 31:38:31 (hh:mm:ss) Elapsed Time : 261 families discovered. RepeatScout/RECON discovery complete: 389 families found Classification Time: 00:25:00 (hh:mm:ss) Elapsed Time Program Time: 37:29:06 (hh:mm:ss) Elapsed Time