RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.CxRrAV/RM_2295004.MonSep81406032025
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: 1757365563
Database = /data/tmp/rModeler.CxRrAV/GCA_001600275.1_JCM_1532_assembly_v001 
  - Sequences = 75
  - Bases = 18637344
Storage Throughput = excellent ( 1556.60 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 18637283 bp ( 18121288 non ambiguous )
   - Num Contigs Represented = 75
   - 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.. : 7 raw families identified
   - RepeatScout: Running filtering stage.. 7 families remaining
   - RepeatScout: 00:00:28 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 7 families... 00:00:05 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:37 (hh:mm:ss) Elapsed Time : 7 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 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       133 repeats masked totaling 18244 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10315989 bp
       Num Contigs Represented = 61
       Non ambiguous bp:
             Initial: 10023043 bp
             After Masking: 9963038 bp
             Masked: 0.60 % 
 -- Input Database Coverage: 10315989 bp out of 18637344 bp ( 55.35 % )
Sampling Time: 00:00:16 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 40470
Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 1581 HSPs Collected
Number of families returned by RECON: 674
Round Time: 00:05:51 (hh:mm:ss) Elapsed Time : 0 families discovered.
   - Increasing sample size to include end piece now = 38637344


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 38637344 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       98 repeats masked totaling 13962 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 8321265 bp
       Num Contigs Represented = 54
       Non ambiguous bp:
             Initial: 8098216 bp
             After Masking: 8052585 bp
             Masked: 0.56 % 
 -- Input Database Coverage: 18637254 bp out of 18637344 bp ( 100.00 % )
Sampling Time: 00:00:14 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 25878
Comparison Time: 00:03:54 (hh:mm:ss) Elapsed Time, 1008 HSPs Collected
Number of families returned by RECON: 473
Round Time: 00:04:23 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 7 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.CxRrAV/RM_2295004.MonSep81406032025
# 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: 00:00:06 (hh:mm:ss) Elapsed Time


Program Time: 00:10:57 (hh:mm:ss) Elapsed Time