This is due to a mismatch is chromosome names between your hg19.len file (UCSC
naming) and the VCF (Ensembl naming). This should be handled better by Galaxy,
and I’ve created a card for it:
https://trello.com/c/bjmNesZj
In the meantime, I used this command to convert chromosome names for this
I am trying to visualise VCF exported from:
ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz
However I get the following error: (Both on Galaxy Main and Local installation)
Input error: Chromosome 1 found in your input file but not in your genome file.
needLargeMem: trying to
Hi Jeremy,
Thank you so much for reply.
You are right…..I just took the first few lines in fastq file and mapped with
bowtie. Now it works with this small dataset.
I am trying to find the error in my complete dataset, but haven't spotted any
yet.
Do you think the error is from reading the
When visualizing a BAM dataset, Galaxy generates a bigwig dataset of read
coverage. Trying to visualize this dataset is causing the issue. You could try
to convert the BAM to BigWig manually (click on dataset's pencil icon --
convert format -- convert to bigwig) and see if there are any issues
Dear all,
I updated to the latest Galaxy stable code, and updated the
datatypes_conf.xml.
Trackster displays an error after opening a saved view:
***
Error: The requested genome file
(/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not
be opened.
Trackster displays an error after opening a saved view:
***
Error: The requested genome file
(/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be
opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open
Hi Jeremy,
Thanks for you assistance. I would love to try your suggestions, but
Galaxy won't start anymore.
I have found the root cause of the problems: my home partition has
become too small, due to a fat 'job_working_directory'. I didn't expect
it to become so big (especially with tophat
Hi Joachim,
It looks like your integrated_tool_panel.xml file has been corrupted somehow.
You can move this file to a backup location (or delete) and it should be
automatically regenerated on Galaxy startup. If this fixes the issue, could you
share a copy of the file? It might be helpful for
1) The dist is most recent:
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 7982:12fcd068b12e
tag: tip
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
2)
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
I've seen this once or twice before but haven't been able to track down the
issue yet.
Here are two workaround that may help you out:
(1) Add the dataset to a
Thanks for your suggestion, Hans-Rudolf. Unfortunately, no success.
Looking into it bit deeper. Keep suggestions coming ;-)
Joachim
On 11/08/2012 05:00 PM, Hans-Rudolf Hotz wrote:
Hi Joachim
This might be completely unrelated, but your situation reminds me of
our case when we did the last
Can you please verify that you're running the most recent dist?
In the most recent dist, requireJS modules are used, so Dataset is prefixed
with its module, e.g.
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Nearly all saved viz's just show a blank main window, while just
displaying the Galaxy header and the trackster header bar.
In contrast, one visualisation gives this error:
ConverterDependencyException: 'A
Try clearing your browser cache and see if that does the trick.
If not, please open your JavaScript console and report the errors that you're
seeing.
Thanks,
J.
On Nov 8, 2012, at 4:56 AM, Joachim Jacob wrote:
Hi all,
After upgrading to the latest galaxy-dist, Trackster does not behave.
Clearing cache did not solve it.
The Js console reports (when trying to visualize an short-read alignment):
Uncaught ReferenceError: Dataset is not defined visualization.js:1
Uncaught ReferenceError: Dataset is not defined tracks.js:1
Uncaught ReferenceError: Dataset is not defined
Hi Joachim
This might be completely unrelated, but your situation reminds me of our
case when we did the last update (to Oct 5th release):
All previously stored visualizations didn't work any more a first. I had
to modify the datatypes_conf.xml file by adding
the following line:
datatype
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the BAM is displayed nicely):
[ti_index_core] bug in BGZF: 80048ed5001b 80048ed5
Thanks for any input,
Joachim
--
Joachim
Can you please share the datasets that are generating this errors?
Thanks,
J.
On Oct 24, 2012, at 4:19 AM, Joachim Jacob wrote:
Hi all,
I want to view two interval-type datasets in trackster on genome hg19
together with one BAM dataset.
The interval datasets give an error (while the
The error you saw was generated by tabix (which is used for fast random access
to interval files), so it's possible that you hit tabix's upper bound. You
might consider following up with the tabix folks to see what the issue is.
As you noted, your dataset is definitely better formatted as a
FYI, trackster supports BigWig directly (no conversion or additional
indexing) and quite efficiently, so you will likely have the most luck
with that.
-- jt
On Wed, Oct 24, 2012 at 3:09 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
bigwig file.
20 matches
Mail list logo
