gtfToGenePred error: Unpaired type(FLH191188.01X;)/val on end of gtf line[...]

[Christian Brueffer]

Hi everyone,

I have a GTF file which produces the following error when fed into
gtfToGenePred (latest from the UCSC website, so v336 I suppose):

~/gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt
ref-transcripts.gtf ref-transcripts.genePred
Unpaired type(FLH191188.01X;)/val on end of gtf line 126843 of
ref-transcripts.gtf

The line in question is the following, and an input file containing
solely this line also provokes the problem:

chr1 hg38_knownGene exon 206586988 206589275 0 + . knownCanonicalChrom
"NA"; RZPDo839A0777D "Ras association (RalGDS/AF-6) domain family 5
(RASSF5) gene, encodes complete protein.""; description ""Synthetic
construct clone IMAGE:100005591"; protAcc; knownCanonicalChromStart
"NA"; knownToRefSeq "NA"; knownIsoformsClusterID "3367"; gene_id
"uc031vlt.1"; alias "DQ892961"; transcript_id "uc031vlt.1"; mRNA
"DQ892961"; knownCanonicalChromEnd "NA"; knownCanonicalClusterId "NA";
refseq; locusLink "NA"; geneSymbol "RASSF5"; FLH191188.01X;

The line looks like valid GTF to me, any idea?

Cheers,

Chris

[Christopher Lee]

Hi Chris,

Thank you for your question about gtfToGenePred.

The 9th field of your GTF file has to start with: 'gene_id "value"; "transcript_id "value";'. I rearranged your problematic GTF line like so:

chr1    hg38_knownGene  exon    206586988       206589275       0       +       .       gene_id "uc031vlt.1"; transcript_id "uc031vlt.1"; knownCanonicalChrom "NA"; RZPDo839A0777D "Ras association (RalGDS/AF-6) domain family 5 (RASSF5) gene, encodes complete protein.""; description ""Synthetic construct clone IMAGE:100005591"; protAcc; knownCanonicalChromStart "NA"; knownToRefSeq "NA"; knownIsoformsClusterID "3367";  alias "DQ892961";  mRNA "DQ892961"; knownCanonicalChromEnd "NA"; knownCanonicalClusterId "NA"; refseq; locusLink "NA";

and gtfToGenePred worked correctly:

$ gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt refTranscripts.gtf refTranscripts.genePred
$ cat refTranscripts.genePred 
uc031vlt.1    chr1    +    206586987    206589275    206589275    206589275    1    206586987,    206589275,    0    uc031vlt.1    none    none    -1,

For more information about the GTF format please see the following:
http://genome.ucsc.edu/FAQ/FAQformat.html#format4
http://mblab.wustl.edu/GTF2.html

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[Christian Brueffer]

Hi Christopher,

that was too obvious, thanks a lot!

Cheers,

Chris

On 2016-08-11 21:07, Christopher Lee wrote:
> Hi Chris,
>
> Thank you for your question about gtfToGenePred.
>
> The 9th field of your GTF file has to start with: 'gene_id "value";
> "transcript_id "value";'. I rearranged your problematic GTF line like so:
>
> chr1 hg38_knownGene exon 206586988 206589275 0 + . gene_id "uc031vlt.1"; transcript_id "uc031vlt.1"; knownCanonicalChrom "NA"; RZPDo839A0777D "Ras association (RalGDS/AF-6) domain family 5 (RASSF5) gene, encodes complete protein.""; description ""Synthetic construct clone IMAGE:100005591"; protAcc; knownCanonicalChromStart "NA"; knownToRefSeq "NA"; knownIsoformsClusterID "3367"; alias "DQ892961"; mRNA "DQ892961"; knownCanonicalChromEnd "NA"; knownCanonicalClusterId "NA"; refseq; locusLink "NA";
>
>
> and gtfToGenePred worked correctly:
>
> $ gtfToGenePred -allErrors -ignoreGroupsWithoutExons -genePredExt refTranscripts.gtf refTranscripts.genePred
> $ cat refTranscripts.genePred
> uc031vlt.1 chr1 + 206586987 206589275 206589275 206589275 1 206586987, 206589275, 0 uc031vlt.1 none none -1,
>
>
> For more information about the GTF format please see the following:
> http://genome.ucsc.edu/FAQ/FAQformat.html#format4
> http://mblab.wustl.edu/GTF2.html
>
> Thank you again for your inquiry and using the UCSC Genome Browser. If
> you have any further
> questions, please reply to gen...@soe.ucsc.edu

> <mailto:gen...@soe.ucsc.edu>. All messages sent to that address are archived

> on a publicly-accessible forum. If your question includes sensitive
> data, you may send it instead

> to genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.

> <mailto:genome%2Bunsu...@soe.ucsc.edu>.
>
>