macmanes/BUSCO_err.md

## BUSCO_err.md

      
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              BUSCO_err.md
            
          
    I am having an issue with running the sample data. I can run with the -l example flag and these results match the expected results, but when I run with -l eukaryota, I get an error, which is detailed below.
python3 ../BUSCO_v1.1b1.py -o euk_test -in target.fa -l eukaryota -m genome -c 10
eukaryota
*** Running tBlastN ***


Building a new DB, current time: 06/17/2015 12:07:21
New DB name:   euk_test
New DB title:  target.fa
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1 sequences in 0.0191998 seconds.
*** Getting coordinates for candidate regions! ***
*** pre-Augustus scaffold extraction ***
*** Running Augustus prediction ***
Starting Thread-1
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*** Error in `augustus': double free or corruption (fasttop): 0x0000000002e96c50 ***
Exiting Thread-9
Exiting Thread-6
Exiting Thread-7
Exiting Thread-8
Exiting Thread-1
Exiting Thread-2
Exiting Thread-10
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Exiting Main Thread
*** Extracting predicted proteins ***
*** Running HMMER to confirm orthology of predicted proteins ***

Error: Sequence file ./run_euk_test//augustus_proteins/47983.fas is empty or misformatted


Error: Sequence file ./run_euk_test//augustus_proteins/87390.fas is empty or misformatted


Error: Sequence file ./run_euk_test//augustus_proteins/87828.fas is empty or misformatted

...

*** Parsing HMMER results ***
Total complete BUSCOs found in assembly (<2 sigma) :  3	(0 duplicated).
Total BUSCOs partially recovered (>2 sigma) :  0
Total groups searched: 429
Total BUSCOs not found:  426
Training augustus gene predictor
Will create parameters for a EUKARYOTIC species!
creating directory /share/augustus-3.1/config/species/euk_test/ ...
creating /share/augustus-3.1/config/species/euk_test/euk_test_parameters.cfg ...
creating /share/augustus-3.1/config/species/euk_test/euk_test_weightmatrix.txt ...
creating /share/augustus-3.1/config/species/euk_test/euk_test_metapars.cfg ...
The necessary files for training euk_test have been created.
Now, either run etraining or optimize_parameters.pl with --species=euk_test.
etraining quickly estimates the parameters from a file with training genes.
optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.

# Read in 2 genbank sequences.
Quantiles of the GC contents in the training set:
0%	0.433
5%	0.433	10%	0.433
15%	0.433	20%	0.433
25%	0.433	30%	0.433
35%	0.433	40%	0.433
45%	0.433	50%	0.433
55%	0.433	60%	0.433
65%	0.433	70%	0.433
75%	0.433	80%	0.433
85%	0.433	90%	0.433
95%	0.433	100%	0.44
HMM-training the parameters...
i= 0 bc= (0.237, 0.263, 0.263, 0.237)
 ** building model for exons *EXON*
start codon frequencies: ATG(2)
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
 number of bases in the reading frames: 696 698 698
--- frame = 0 ---    minPatSum = 233
--- frame = 1 ---    minPatSum = 233
--- frame = 2 ---    minPatSum = 233
--- initial frame = 0 ---    minPatSum = 233
--- initial frame = 1 ---    minPatSum = 233
--- initial frame = 2 ---    minPatSum = 233
--- internal exon terminal frame = 0 ---    minPatSum = 233
--- internal exon terminal frame = 1 ---    minPatSum = 233
--- internal exon terminal frame = 2 ---    minPatSum = 233
single, initial, internal, terminal mean exon lengths :
765	189	142	234
single exon : 1
initial exon 0 : 1
initial exon 1 : 0
initial exon 2 : 0
internal exon 0 : 6
internal exon 1 : 0
internal exon 2 : 1
terminal exon : 1
Frequency of stop codons:
tag:    0 (0)
taa:    1 (0.5)
tga:    1 (0.5)
end *EXON*
Storing parameters to file...
Writing exon model parameters [1] to file /share/augustus-3.1/config/species/euk_test/euk_test_exon_probs.pbl.
*** Re-running failed predictions with different constraints, total number 426 ***
Starting to run Augustus again....
Starting Thread-1
Starting Thread-2
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Starting Thread-10

*** Error in `augustus': double free or corruption (fasttop): 0x0000000001a973a0 ***
Exiting Thread-10
Exiting Thread-4
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Exiting Thread-7
Exiting Thread-1
Exiting Thread-6
Exiting Thread-3
Exiting Thread-8
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Exiting Main Thread
Starting to run SED....
Starting Thread-1
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Starting Thread-8
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Exiting Thread-1
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Exiting Main Thread
Starting to run EXTRACT....
Starting to run HMMER....
Starting Thread-1
Starting Thread-2
Starting Thread-3
Starting Thread-4
Starting Thread-5
Starting Thread-6
Starting Thread-7
Starting Thread-8
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Starting Thread-10

Error: Sequence file ./run_euk_test//augustus_proteins/27931.fas is empty or misformatted


Error: Sequence file ./run_euk_test//augustus_proteins/37784.fas is empty or misformatted

...

Exiting Thread-9
Exiting Thread-10
Exiting Thread-2
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Exiting Thread-1
Exiting Thread-6
Exiting Thread-3
Exiting Thread-8
Exiting Thread-5
Exiting Thread-7
Exiting Main Thread
Total running time:   390.84869170188904 seconds
Total complete BUSCOs found in assembly (<2 sigma) :  3	(0 duplicated).
Total BUSCOs partially recovered (>2 sigma) :  0
Total groups searched: 429
Total BUSCOs not found:  426


Indeed, when I look at these .fas files that are reported empty they are indeed empty.
l ./run_euk_test//augustus_proteins/37784.fas
-rw-r--r-- 1 macmanes macmanes 0 Jun 17 12:13 ./run_euk_test//augustus_proteins/37784.fas

Just confused as why this would run with the sample lineage but not with the eukaryote lineage..
Please advise.