RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.J0Iy0g/RM_1317880.FriSep120046432025
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: 1757663203
Database = /data/tmp/rModeler.J0Iy0g/GCA_029405325.1_ASM2940532v1 
  - Sequences = 14
  - Bases = 34222199
Storage Throughput = excellent ( 1593.12 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 34222131 bp ( 34222131 non ambiguous )
   - Num Contigs Represented = 14
   - 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.. : 399 raw families identified
   - RepeatScout: Running filtering stage.. 390 families remaining
   - RepeatScout: 00:02:11 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 385 families... 00:49:30 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 6 satellite(s), 138 contained, found in 00:00:06 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:06 (hh:mm:ss) Elapsed Time
Round Time: 00:51:53 (hh:mm:ss) Elapsed Time : 242 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 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       5693 repeats masked totaling 1818259 bp(s).
   - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10013226 bp
       Num Contigs Represented = 13
       Non ambiguous bp:
             Initial: 10013226 bp
             After Masking: 8134919 bp
             Masked: 18.76 % 
 -- Input Database Coverage: 10013226 bp out of 34222199 bp ( 29.26 % )
Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 32131
Comparison Time: 00:03:49 (hh:mm:ss) Elapsed Time, 5759 HSPs Collected
Number of families returned by RECON: 918
Round Time: 00:05:14 (hh:mm:ss) Elapsed Time : 11 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 00:00:21 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       14320 repeats masked totaling 4691455 bp(s).
   - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 24208825 bp
       Num Contigs Represented = 14
       Non ambiguous bp:
             Initial: 24208825 bp
             After Masking: 19365361 bp
             Masked: 20.01 % 
 -- Input Database Coverage: 34222051 bp out of 34222199 bp ( 100.00 % )
Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 186355
Comparison Time: 00:12:16 (hh:mm:ss) Elapsed Time, 18797 HSPs Collected
Number of families returned by RECON: 2700
Round Time: 00:13:58 (hh:mm:ss) Elapsed Time : 34 families discovered.

RepeatScout/RECON discovery complete: 287 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.J0Iy0g/RM_1317880.FriSep120046432025
# 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: 00:01:20 (hh:mm:ss) Elapsed Time


Program Time: 01:12:25 (hh:mm:ss) Elapsed Time