Trackster Visualization error (bedGraphToBigWig Syntax error)

Question: Trackster Visualization error (bedGraphToBigWig Syntax error)

3.7 years ago by

Singapore

jchen015 • 80 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

visualization trackster bedgraphtobigwig • 1.4k views

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modified 2.8 years ago by c.proukakis • 0 • written 3.7 years ago by jchen015 • 80

3.7 years ago by

jgoecks • 10

United States

jgoecks • 10 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,

ADD COMMENT • link written 3.7 years ago by jgoecks • 10

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 REPLY • link written 3.7 years ago by jchen015 • 80

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,

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by jgoecks • 10

3.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.7 years ago by jchen015 • 80

2.8 years ago by

c.proukakis • 0

c.proukakis • 0 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 COMMENT • link written 2.8 years ago by c.proukakis • 0

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