Question: Trackster Visualization error (bedGraphToBigWig Syntax error)
0
gravatar for jchen015
3.3 years ago by
jchen01580
Singapore
jchen01580 wrote:
Hi all

So my intention is to get my (.bam) file visualized on my local Galaxy.

I got all my .len files from the execution of the below command:
cd <GALAXY_HOME_DIR>
mkdir ./tool-data/shared/ucsc/chrom/
python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/

Now I have all the reference genome as shown in the Public Galaxy server

     This is the screenshot ( https://www.dropbox.com/s/4lgmz63mxh8czu5/reference_genome.png?dl=0 )

So knowing that my reference genome is hg19 , I chosen it and when I proceeded to add an existing (.bam) which is already in my History for visualizing
  
   This is the screenshot ( https://www.dropbox.com/s/0yqkke5xsamg0o5/upload_dataset.png?dl=0 )

After which, an error occured. 
"
/usr/bin/bedGraphToBigWig: 3: /usr/bin/bedGraphToBigWig: Syntax error: Unterminated quoted string

"
This is the screen shot ( https://www.dropbox.com/s/gru47o5qfzdehw9/error.png?dl=0 ).


my $PATH is

/usr/bin/faToTwoBit:/usr/bin/wigToBigWig:/usr/bin/bedGraphToBigWig:/usr/bin/bedtools:/usr/bin/samtools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/bin/htseq-count


which i presume there is no syntax error....

 

 

May I know what is the issue over here?

 

Regards,

Julius

ADD COMMENTlink modified 2.4 years ago by c.proukakis0 • written 3.3 years ago by jchen01580
1
gravatar for jgoecks
3.3 years ago by
jgoecks10
United States
jgoecks10 wrote:

Julius,

I think you have to set the dbkey for the dataset before using it in Trackster. Try going to your history, clicking on pencil icon for the dataset that you want to visualize, and setting the database build to hg19. IIRC, there's a bug that allows datasets without a dbkey to be added to Trackster; this used to work but then was broken a ways back. If this workaround is successful for you, we'll file a bug report and get it fixed eventually.

Best,

J.

ADD COMMENTlink written 3.3 years ago by jgoecks10

Hi jgoecks

Thanks for the suggestion.

I followed your suggestion as follows (https://www.dropbox.com/s/mx2x5jvlwcjybjp/seting_db_build.png?dl=0 ).

After which, I restarted Galaxy but the error still persist....

/usr/bin/bedGraphToBigWig: 3: /usr/bin/bedGraphToBigWig: Syntax error: Unterminated quoted string
ADD REPLYlink written 3.3 years ago by jchen01580

Sorry to hear about the continuing issue Julius. Can you try showing hidden datasets (using the link below the history title), find a failed converter job, expand it, and click on the bug icon to see the full command line? What is that command line?

Thanks,

J.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by jgoecks10
1
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello Julius,

This may be a memory issue. Meaning that your local does not have enough memory to perform the operation. Are you able to visualize the same dataset on Main?

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k

Hi Jen

When I visualize on the public Galaxy, there is an error stating :

"

chr1 is not found in chromosome sizes file

"

For the previous time, this file seems to be working well. (as shown here: https://www.dropbox.com/s/707g9samrpsn3d8/visualization.png?dl=0 ).

Is it the Galaxy problem here? I think these 2 problems has no relation (the one on my local galaxy and main).

 

Regards

Julius

 

ADD REPLYlink written 3.3 years ago by jchen01580
0
gravatar for c.proukakis
2.4 years ago by
c.proukakis0 wrote:

I am having  the same error when trying to run a bam file on trackster on the galaxy server

1 is not found in chromosome sizes file

I am a complete novice in this, have tried and failed to install circos, so if someone can help I will be most grateful

ADD COMMENTlink written 2.4 years ago by c.proukakis0
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