Can't locate 'setThreadByQuery' via package "NCBIBlastSearchEngine" at RepeatModeler/Refiner #220
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Hi folks,
I have been attempting to load in RepeatModeler through your usual installation description and am running into this one main issue I can't figure out.
I am on a campus cluster so I'm not sure if I have the proper root access I might need to remedy this.
I am not honest how I can reproduce this error for you, but it comes through running the RepeatModeler program on my genomes.
The BuildDatabase program runs just fine.
My error as mentioned in my subject keeps indicating the setThreadByQuery function cannot be found in my NCBIBlastSearchEngine program when running RepeatModeler/Refiner. All programs are in my RepeatModeler/bin directory of which I have configured to through your configuration steps.
I've done what I could, updated programs, created a conda environment with RepeatModeler and added all the dependent programs into the same environment, ran configure on different directories of each program, ran configure on one main directory where all the dependent programs were copied into, and etc scenario.
If I let the program run to completion it always fails and never generates my .fa or .stk files I need to progress with my analysis. Please let me know what I can do to remedy this.
Thank you!
My copied error looks like this.
Sequences = 95
Bases = 5675239
Storage Throughput = fair ( 390.19 MB/s )
Ready to start the sampling process.
INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly
and the repetitive content of the sequences. It is not imperative
that RepeatModeler completes all rounds in order to obtain useful
results. At the completion of each round, the files ( consensi.fa, and
families.stk ) found in:
/work/users/t/a/taniak/Annotation/RM_2590771.MonOct231255012023/
will contain all results produced thus far. These files may be
manually copied and run through RepeatClassifier should the program
be terminated early.
RepeatModeler Round # 1
Searching for Repeats
-- Sampling from the database...
Gathering up to 40000000 bp
Final Sample Size = 5675160 bp ( 5667012 non ambiguous )
Num Contigs Represented = 95
Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
RepeatScout: Running build_lmer_table ( l = 13 )..
RepeatScout: Running RepeatScout.. : 95 raw families identified
RepeatScout: Running filtering stage.. 90 families remaining
RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time
Large Satellite Filtering.. : 3 found in 00:00:15 (hh:mm:ss) Elapsed Time
Collecting repeat instances...slurmstepd: error: *** JOB 20955013 ON c0310 CANCELLED AT 2023-10-23T12:57:01 ***
(base) [taniak@longleaf-login4 logs]$ cat repeatmodeler_attempt.17.log
Histoplasma_capsulatum_HcMZ5
Building database repeat_library/Histoplasma_capsulatum_HcMZ5:
Reading genomes/Histoplasma_capsulatum_HcMZ5.sorted.fasta...
Number of sequences (bp) added to database: 999 ( 14298302 bp )
RepeatModeler Version 2.0.5
Using output directory = /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023
Search Engine = rmblast 2.14.1+
Threads = 4
Dependencies: TRF 4.10, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.5
LTR Structural Analysis: Enabled ( GenomeTools 1.6.2, LTR_Retriever v2.9.5,
Ninja 0.97-cluster_only, MAFFT 7.490,
CD-HIT 4.8.1 )
Random Number Seed: 1698000022
Database = /work/users/t/a/taniak/Annotation/repeat_library/Histoplasma_capsulatum_HcMZ5 .
Sequences = 999
Bases = 14298302
N50 = 1923913
Contig Histogram:
Size(bp) Count
2296636-2460646 | [ 1 ]
2132626-2296635 | [ ]
1968616-2132625 | [ 1 ]
1804607-1968616 | [ 1 ]
1640597-1804606 | [ ]
1476587-1640596 | [ ]
1312577-1476586 | [ ]
1148568-1312577 | [ 2 ]
984558-1148567 | [ 1 ]
820548-984557 | [ ]
656538-820547 | [ ]
492529-656538 | [ ]
328519-492528 | [ ]
164509-328518 | [ ]
500-164509 |************************************************** [ 993 ]
Storage Throughput = fair ( 332.84 MB/s )
Ready to start the sampling process.
INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly
and the repetitive content of the sequences. It is not imperative
that RepeatModeler completes all rounds in order to obtain useful
results. At the completion of each round, the files ( consensi.fa, and
families.stk ) found in:
/work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/
will contain all results produced thus far. These files may be
manually copied and run through RepeatClassifier should the program
be terminated early.
RepeatModeler Round # 1
Searching for Repeats
-- Sampling from the database...
Gathering up to 40000000 bp
Final Sample Size = 14298197 bp ( 14255281 non ambiguous )
Num Contigs Represented = 999
Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
-- Running RepeatScout on the sequences...
RepeatScout: Running build_lmer_table ( l = 13 )..
RepeatScout: Running RepeatScout.. : 155 raw families identified
RepeatScout: Running filtering stage.. 146 families remaining
RepeatScout: 00:03:32 (hh:mm:ss) Elapsed Time
Large Satellite Filtering.. : 4 found in 00:00:05 (hh:mm:ss) Elapsed Time
Collecting repeat instances...: 00:02:44 (hh:mm:ss) Elapsed Time
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Refinement: 00:18:30 (hh:mm:ss) Elapsed Time
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-28.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-23.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-11.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-39.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-45.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-47.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-22.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-41.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-0.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-48.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-33.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-3.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-5.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-30.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-8.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-18.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-16.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-6.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-25.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-12.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-20.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-27.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-1.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-36.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-19.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-21.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-15.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-24.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-50.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-26.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-44.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-37.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-49.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-2.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-43.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-9.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-38.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-31.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-40.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-14.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-4.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-13.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-52.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-34.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-46.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-51.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-29.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-17.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-10.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-35.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-7.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-42.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-32.fa.
Family Refinement: 00:18:30 (hh:mm:ss) Elapsed Time
Round Time: 00:24:53 (hh:mm:ss) Elapsed Time : 0 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...
851 Tandem Repeats Masked
TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 10030276 bp
Num Contigs Represented = 669
Non ambiguous bp:
Initial: 10001027 bp
After Masking: 9951556 bp
Masked: 0.49 %
-- Input Database Coverage: 10030276 bp out of 14298302 bp ( 70.15 % )
Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
Total Comparisons = 354061
1% completed, 01:1:09 (hh:mm:ss) est. time remaining.
1% completed, 01:8:13 (hh:mm:ss) est. time remaining.
2% completed, 00:53:43 (hh:mm:ss) est. time remaining.
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6% completed, 00:45:59 (hh:mm:ss) est. time remaining.
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7% completed, 00:44:37 (hh:mm:ss) est. time remaining.
8% completed, 00:55:15 (hh:mm:ss) est. time remaining.
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12% completed, 00:47:49 (hh:mm:ss) est. time remaining.
12% completed, 00:46:58 (hh:mm:ss) est. time remaining.
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14% completed, 00:46:03 (hh:mm:ss) est. time remaining.
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17% completed, 00:41:54 (hh:mm:ss) est. time remaining.
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22% completed, 00:36:15 (hh:mm:ss) est. time remaining.
23% completed, 00:39:28 (hh:mm:ss) est. time remaining.
25% completed, 00:37:27 (hh:mm:ss) est. time remaining.
25% completed, 00:37:21 (hh:mm:ss) est. time remaining.
25% completed, 00:37:17 (hh:mm:ss) est. time remaining.
26% completed, 00:36:56 (hh:mm:ss) est. time remaining.
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99% completed, 00:0:09 (hh:mm:ss) est. time remaining.
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99% completed, 00:0:02 (hh:mm:ss) est. time remaining.
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99% completed, 00:0:01 (hh:mm:ss) est. time remaining.
99% completed, 00:0:01 (hh:mm:ss) est. time remaining.
99% completed, 00:0:01 (hh:mm:ss) est. time remaining.
99% completed, 00:0:01 (hh:mm:ss) est. time remaining.
99% completed, 00:0:01 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
100% completed, 00:0:00 (hh:mm:ss) est. time remaining.
Comparison Time: 00:52:11 (hh:mm:ss) Elapsed Time, 512525 HSPs Collected
RECON: Running imagespread..
RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time
RECON: Running initial definition of elements ( eledef )..
RECON Elapsed: 00:01:01 (hh:mm:ss) Elapsed Time
RECON: Running re-definition of elements ( eleredef )..
RECON Elapsed: 00:04:10 (hh:mm:ss) Elapsed Time
RECON: Running re-definition of edges ( edgeredef )..
RECON Elapsed: 00:03:54 (hh:mm:ss) Elapsed Time
RECON: Running family definition ( famdef )..
RECON Elapsed: 00:00:02 (hh:mm:ss) Elapsed Time
Obtaining element sequences
Number of families returned by RECON: 634
Processing families with greater than 15 elements
Instance Gathering: 00:00:01 (hh:mm:ss) Elapsed Time
Refining 15 families
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-253.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-87.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-51.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-20.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-22.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-41.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-27.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-74.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-19.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-26.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-133.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-89.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-319.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-43.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-63.fa.
Family Refinement: 00:33:32 (hh:mm:ss) Elapsed Time
Round Time: 01:35:42 (hh:mm:ss) Elapsed Time : 0 families discovered.
Increasing sample size to include end piece now = 34298302
RepeatModeler Round # 3
Searching for Repeats
-- Sampling from the database...
Gathering up to 34298302 bp
Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time
-- Running TRFMask on the sequence...
372 Tandem Repeats Masked
TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time
-- Sample Stats:
Sample Size 4267842 bp
Num Contigs Represented = 338
Non ambiguous bp:
Initial: 4254175 bp
After Masking: 4232204 bp
Masked: 0.52 %
-- Input Database Coverage: 14298118 bp out of 14298302 bp ( 100.00 % )
Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
Total Comparisons = 82621
0% completed, 00:10:07 (hh:mm:ss) est. time remaining.
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54% completed, 00:4:10 (hh:mm:ss) est. time remaining.
56% completed, 00:4:01 (hh:mm:ss) est. time remaining.
57% completed, 00:3:58 (hh:mm:ss) est. time remaining.
57% completed, 00:4:03 (hh:mm:ss) est. time remaining.
57% completed, 00:4:00 (hh:mm:ss) est. time remaining.
57% completed, 00:3:59 (hh:mm:ss) est. time remaining.
58% completed, 00:3:58 (hh:mm:ss) est. time remaining.
59% completed, 00:3:50 (hh:mm:ss) est. time remaining.
59% completed, 00:3:49 (hh:mm:ss) est. time remaining.
64% completed, 00:3:13 (hh:mm:ss) est. time remaining.
64% completed, 00:3:11 (hh:mm:ss) est. time remaining.
65% completed, 00:3:06 (hh:mm:ss) est. time remaining.
66% completed, 00:3:00 (hh:mm:ss) est. time remaining.
67% completed, 00:2:55 (hh:mm:ss) est. time remaining.
67% completed, 00:2:53 (hh:mm:ss) est. time remaining.
68% completed, 00:2:55 (hh:mm:ss) est. time remaining.
68% completed, 00:2:51 (hh:mm:ss) est. time remaining.
69% completed, 00:2:49 (hh:mm:ss) est. time remaining.
69% completed, 00:2:48 (hh:mm:ss) est. time remaining.
72% completed, 00:2:35 (hh:mm:ss) est. time remaining.
72% completed, 00:2:30 (hh:mm:ss) est. time remaining.
73% completed, 00:2:26 (hh:mm:ss) est. time remaining.
73% completed, 00:2:25 (hh:mm:ss) est. time remaining.
74% completed, 00:2:23 (hh:mm:ss) est. time remaining.
74% completed, 00:2:23 (hh:mm:ss) est. time remaining.
75% completed, 00:2:19 (hh:mm:ss) est. time remaining.
76% completed, 00:2:13 (hh:mm:ss) est. time remaining.
78% completed, 00:1:58 (hh:mm:ss) est. time remaining.
78% completed, 00:1:57 (hh:mm:ss) est. time remaining.
78% completed, 00:1:56 (hh:mm:ss) est. time remaining.
80% completed, 00:1:48 (hh:mm:ss) est. time remaining.
81% completed, 00:1:42 (hh:mm:ss) est. time remaining.
81% completed, 00:1:41 (hh:mm:ss) est. time remaining.
83% completed, 00:1:32 (hh:mm:ss) est. time remaining.
83% completed, 00:1:31 (hh:mm:ss) est. time remaining.
83% completed, 00:1:30 (hh:mm:ss) est. time remaining.
84% completed, 00:1:29 (hh:mm:ss) est. time remaining.
84% completed, 00:1:25 (hh:mm:ss) est. time remaining.
87% completed, 00:1:14 (hh:mm:ss) est. time remaining.
88% completed, 00:1:09 (hh:mm:ss) est. time remaining.
88% completed, 00:1:09 (hh:mm:ss) est. time remaining.
88% completed, 00:1:05 (hh:mm:ss) est. time remaining.
89% completed, 00:1:04 (hh:mm:ss) est. time remaining.
89% completed, 00:1:03 (hh:mm:ss) est. time remaining.
89% completed, 00:1:02 (hh:mm:ss) est. time remaining.
89% completed, 00:1:02 (hh:mm:ss) est. time remaining.
89% completed, 00:1:01 (hh:mm:ss) est. time remaining.
89% completed, 00:1:00 (hh:mm:ss) est. time remaining.
90% completed, 00:0:56 (hh:mm:ss) est. time remaining.
90% completed, 00:0:55 (hh:mm:ss) est. time remaining.
91% completed, 00:0:52 (hh:mm:ss) est. time remaining.
92% completed, 00:0:46 (hh:mm:ss) est. time remaining.
93% completed, 00:0:41 (hh:mm:ss) est. time remaining.
93% completed, 00:0:37 (hh:mm:ss) est. time remaining.
94% completed, 00:0:32 (hh:mm:ss) est. time remaining.
94% completed, 00:0:32 (hh:mm:ss) est. time remaining.
95% completed, 00:0:28 (hh:mm:ss) est. time remaining.
96% completed, 00:0:22 (hh:mm:ss) est. time remaining.
96% completed, 00:0:18 (hh:mm:ss) est. time remaining.
97% completed, 00:0:13 (hh:mm:ss) est. time remaining.
97% completed, 00:0:13 (hh:mm:ss) est. time remaining.
97% completed, 00:0:12 (hh:mm:ss) est. time remaining.
97% completed, 00:0:12 (hh:mm:ss) est. time remaining.
98% completed, 00:0:10 (hh:mm:ss) est. time remaining.
98% completed, 00:0:08 (hh:mm:ss) est. time remaining.
98% completed, 00:0:08 (hh:mm:ss) est. time remaining.
98% completed, 00:0:07 (hh:mm:ss) est. time remaining.
99% completed, 00:0:05 (hh:mm:ss) est. time remaining.
99% completed, 00:0:05 (hh:mm:ss) est. time remaining.
99% completed, 00:0:04 (hh:mm:ss) est. time remaining.
99% completed, 00:0:02 (hh:mm:ss) est. time remaining.
99% completed, 00:0:01 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
99% completed, 00:0:00 (hh:mm:ss) est. time remaining.
100% completed, 00:0:00 (hh:mm:ss) est. time remaining.
Comparison Time: 00:10:15 (hh:mm:ss) Elapsed Time, 125632 HSPs Collected
RECON: Running imagespread..
RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time
RECON: Running initial definition of elements ( eledef )..
RECON Elapsed: 00:00:14 (hh:mm:ss) Elapsed Time
RECON: Running re-definition of elements ( eleredef )..
RECON Elapsed: 00:00:50 (hh:mm:ss) Elapsed Time
RECON: Running re-definition of edges ( edgeredef )..
RECON Elapsed: 00:01:11 (hh:mm:ss) Elapsed Time
RECON: Running family definition ( famdef )..
RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time
Obtaining element sequences
Number of families returned by RECON: 237
Processing families with greater than 15 elements
Instance Gathering: 00:00:00 (hh:mm:ss) Elapsed Time
Refining 5 families
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-10.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-14.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-27.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-3.fa.
WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-45.fa.
Family Refinement: 00:34:43 (hh:mm:ss) Elapsed Time
Round Time: 00:47:33 (hh:mm:ss) Elapsed Time : 0 families discovered.
RepeatScout/RECON discovery complete: 0 families found
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