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hillerlab / CESAR2.0

MIT License
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Hi, #5

Closed sychensau closed 6 years ago

sychensau commented 6 years ago

I just tested the mini example of cesar2 according to the recommended steps and found an error reported below. Is this an error for the gb file? Thanks for your attentions.

Incorrent format 'POLR3K chr16 - 46406 53628 47429 53586 47429-47557,51557-51645,53475-53586' should have minimum 10 fields, found only 8 Can't locate Scalar/Util/Numeric.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/csy/Downloads/CESAR2.0/tools/annotateGenesViaCESAR.pl line 8. BEGIN failed--compilation aborted at /home/csy/Downloads/CESAR2.0/tools/annotateGenesViaCESAR.pl line 8. ./jobListGenePred: line 1: /home/csy/projects/cesarTest/geneAnnotation/echo: No such file or directory sed: -e expression #1, char 7: unterminated s' command sed: -e expression #1, char 4: unterminateds' command wrongs # args /home/csy/Downloads/CESAR2.0/tools/bed2GenePred.pl - Convert CESAR2.0 annotated exons (as elements in a bed file) to a genePred file

MichaelHiller commented 6 years ago

Hi,

it seems that you called formatGenePred.pl with twoGenes.gp.forCESAR as input, since the error message comes from this script.

twoGenes.gp.forCESAR is not a proper genePred format, which formatGenePred.pl would require as input (with 10 fields). Instead twoGenes.gp.forCESAR is the output of formatGenePred.pl and can be directly used with annotateGenesViaCESAR.pl. I just copy/pasted the miniExample exactly as is and this works.

It also seems that you don't have https://metacpan.org/pod/Scalar::Util::Numeric installed. Please let me know if problems remain.

Michael