Fontconfig error

[ghg296]

Hi,

I am attempting to run the triplet periodicity test for my data. I have managed to upload my .sam file and convert it to the R input format. Unfortunately, when running the periodicity tool the program crashes and returns a Fontconfig error stating it could not load the default config file. Since fontconfig usually deals with whatever font the data is written in, I am a bit confused about how to fix this error, as my transcriptome data is simply imported as a fasta file. Please help me with any potential solutions.

George

[audrey]

(13-Jul-2015 05:48 PM)ghg296 Wrote:  Hi,

I am attempting to run the triplet periodicity test for my data. I have managed to upload my .sam file and convert it to the R input format. Unfortunately, when running the periodicity tool the program crashes and returns a Fontconfig error stating it could not load the default config file. Since fontconfig usually deals with whatever font the data is written in, I am a bit confused about how to fix this error, as my transcriptome data is simply imported as a fasta file. Please help me with any potential solutions.

George

Hi,

Unfortunately we am not familiar with the error that you have reported and so we are not able to offer an immediate solution to this issue. However, we will look into it and try to fix it. Could you let us know which alignment tool you used for aligning your ribo-seq data?

As a possible workaround, you could try generating a .sam file from within RiboGalaxy by uploading your raw FASTQ file and your transcriptome FASTA file and aligning your ribo-seq data using the bowtie implementation in RiboGalaxy (you may need to pre-process the data first by removing the adaptor sequence and removing reads that align to rRNA sequences). The output can then be converted into the format required for riboSeqR.

In the meantime, we will investigate the issue that you report.

Thanks,
RiboGalaxy team

[jamesp]

Hi George,
you could try to set the database type i.e. genome of the file you uploaded and then run the whole job again. To modify the database, use "Edit Attributes" by clicking on the pencil icon of the uploaded file in your history. Then select the appropriate Database/Build from the drop-down and click Save. Then run the periodicity tool again and post your result.

Thanks
jamesp

[ghg296]

(14-Jul-2015 08:17 AM)audrey Wrote:  

(13-Jul-2015 05:48 PM)ghg296 Wrote:  Hi,

I am attempting to run the triplet periodicity test for my data. I have managed to upload my .sam file and convert it to the R input format. Unfortunately, when running the periodicity tool the program crashes and returns a Fontconfig error stating it could not load the default config file. Since fontconfig usually deals with whatever font the data is written in, I am a bit confused about how to fix this error, as my transcriptome data is simply imported as a fasta file. Please help me with any potential solutions.

George

Hi,

Unfortunately we am not familiar with the error that you have reported and so we are not able to offer an immediate solution to this issue. However, we will look into it and try to fix it. Could you let us know which alignment tool you used for aligning your ribo-seq data?

As a possible workaround, you could try generating a .sam file from within RiboGalaxy by uploading your raw FASTQ file and your transcriptome FASTA file and aligning your ribo-seq data using the bowtie implementation in RiboGalaxy (you may need to pre-process the data first by removing the adaptor sequence and removing reads that align to rRNA sequences). The output can then be converted into the format required for riboSeqR.

In the meantime, we will investigate the issue that you report.

Thanks,
RiboGalaxy team

I used bowtie to align my reads to the Arabidopsis TAIR10 genome.

George

---

(14-Jul-2015 02:58 PM)jamesp Wrote:  Hi George,
you could try to set the database type i.e. genome of the file you uploaded and then run the whole job again. To modify the database, use "Edit Attributes" by clicking on the pencil icon of the uploaded file in your history. Then select the appropriate Database/Build from the drop-down and click Save. Then run the periodicity tool again and post your result.

Thanks
jamesp

This did not change anything.

This is my stdout:
Read 731694 items
Calling frames..........done!

This is the stderr:
Fontconfig error: Cannot load default config file

thanks,

George

[vimalkumarvelayudhan]

The Fontconfig message is produced with all output currently where plots are generated. It is not an error in itself.

Could you try generating an alignment and using the output (SAM) instead as Audrey had mentioned in post #2?

It is necessary that the transcript ID's in the SAM file match the FASTA headers in the transcriptome for the Triplet periodicity tool to produce the right output. By doing the alignment as above, this is taken care of automatically.