Cancer Genome Project Software
| Question |
Answer |
| Standalone AutoCSA has failed with an exception but I don't understand it |
There are many possible causes of an exception and we are aware that some error messages may not be
informative. If you encounter such a problem we would like to improve these messages. To do this
we require the following information:
- An example file name for both variant and reference AB1 files
- The standaloneCsa.properties file
- The amplimer.properties file
Please send this information to cgpit@sanger.ac.uk
with a subject of 'REQUEST: Unhelpful exception'.
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Standalone AutoCSA has failed with the following exception;
org.biojava.bio.symbol.IllegalSymbolException: Can't decode token ? into DNA
(where ? is not one of
A,C,G,T,N) this can occur as some basecalling programs use non ACGTN characters in their basecall.
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The only solution in this case is to replace the non ACGTN characters in the basecall held within the ab1
trace file. This may be acomplished with the following perl code which should be run from the command line
(n.b. requires the ABIF perl module available from CPAN).
ls *.ab1 | perl -MABIF -ne 'print; chomp;
$abif = Bio::Trace::ABIF->new(); $abif->open_abif($_,1); $seq =
$abif->sequence; $seq =~ tr/ACGT/N/c; $abif->write_tag('PBAS', $_,\$seq)
for 1,2; $abif->close_abif;'
Thanks to Avishay Vaknin (Compugen) for this solution.
|
Standalone AutoCSA has failed with the following exception;
WARN uk.ac.sanger.cgp.autocsa.util.ConvertTrace - Caught IOException:
.\resources\mobCorrFiles\KB_3730_POP7_BDTv3.mob (The system cannot find the file specified)
WARN uk.ac.sanger.cgp.autocsa.util.ConvertTrace - mobilityCorrect: problem reading mobfile
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The problem here is that autoCSA cannot locate the required Mobility Correction datafile as set in your
ab1 trace files. We have included a Mobility Correction file as used by our systems (DT3730POP7=BDv3.mob),
you can copy this file
to the file required on your system (in directory .\resources\mobCorrFiles), with;
cp "DT3730POP7=BDv3.mob"
"KB_3730_POP7_BDTv3.mob" (in this case but probably a different filename in you case).
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