RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.muLPL1/RM_1305908.MonSep81344192025 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1757364258 Database = /dev/shm/rModeler.muLPL1/GCA_001443065.1_ASM144306v1 - Sequences = 57309 - Bases = 129776072 - N50 = 2935 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29928-32052 | [ 1 ] 27805-29928 | [ ] 25681-27804 | [ 1 ] 23558-25681 | [ 3 ] 21434-23557 | [ 5 ] 19311-21434 | [ 5 ] 17187-19310 | [ 17 ] 15064-17187 | [ 32 ] 12940-15063 | [ 91 ] 10817-12940 | [ 237 ] 8693-10816 | [ 553 ] 6570-8693 |* [ 1474 ] 4446-6569 |**** [ 3837 ] 2323-4446 |************** [ 11280 ] 200-2323 |************************************************** [ 39773 ] 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 = excellent ( 1655.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42772259 bp ( 40001589 non ambiguous ) - Num Contigs Represented = 18976 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 136 raw families identified - RepeatScout: Running filtering stage.. 116 families remaining - RepeatScout: 00:03:13 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 115 families... 00:00:17 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 19 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:03:35 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4775 repeats masked totaling 1172436 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10691666 bp Num Contigs Represented = 4667 Non ambiguous bp: Initial: 10001950 bp After Masking: 8832590 bp Masked: 11.69 % -- Input Database Coverage: 10691666 bp out of 129776072 bp ( 8.24 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 10888111 Comparison Time: 00:20:20 (hh:mm:ss) Elapsed Time, 22606 HSPs Collected Number of families returned by RECON: 1760 Round Time: 00:21:28 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (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... 19721 repeats masked totaling 6818290 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32081208 bp Num Contigs Represented = 14310 Non ambiguous bp: Initial: 30000123 bp After Masking: 23265417 bp Masked: 22.45 % -- Input Database Coverage: 42772874 bp out of 129776072 bp ( 32.96 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 102380895 Comparison Time: 01:12:17 (hh:mm:ss) Elapsed Time, 90999 HSPs Collected Number of families returned by RECON: 4626 Round Time: 01:15:43 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78104 repeats masked totaling 29754655 bp(s). - TE Masking time 00:03:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 87003008 bp Num Contigs Represented = 38332 Non ambiguous bp: Initial: 81347706 bp After Masking: 52083399 bp Masked: 35.97 % -- Input Database Coverage: 129775882 bp out of 129776072 bp ( 100.00 % ) Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 734651946 Comparison Time: 04:07:29 (hh:mm:ss) Elapsed Time, 201664 HSPs Collected Number of families returned by RECON: 10857 Round Time: 04:18:22 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatScout/RECON discovery complete: 690 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.muLPL1/RM_1305908.MonSep81344192025 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:01:55 (hh:mm:ss) Elapsed Time Program Time: 06:01:03 (hh:mm:ss) Elapsed Time