Question

Question: Can't import or generate ref Flat

0

3.3 years ago by

United States

Hi,

We are running a local galaxy instance and I am having trouble important or grabbing a refFlat-formatted hg19 annotation. I have tried importing the same annotations I used on Usegalaxy as well as grabbing new from UCSC Main and neither work. I am not a developer, so I cannot decode the error call below (and the person here who does that is trying to help, but very very busy). I WAS able to import a mm10 refFlat and grab from UCSC main, so it seems to be annotation-dependent. Does anyone have any idea what is wrong here or how to address it?

Thanks,

Brian

The Galaxy framework encountered the following error while attempting to run the tool:

Traceback (most recent call last):

File "/var/local/galaxy-site/lib/galaxy/jobs/runners/local.py", line 129, in queue_job

job_wrapper.finish( stdout, stderr, exit_code )

File "/var/local/galaxy-site/lib/galaxy/jobs/__init__.py", line 1200, in finish

dataset.datatype.set_meta( dataset, overwrite=False )

File "/var/local/galaxy-site/lib/galaxy/datatypes/tabular.py", line 919, in set_meta

raise ('mismatching number of columns in header and data')

TypeError: exceptions must be old-style classes or derived from BaseException, not str

Tool execution generated the following error message:

Unable to finish job

galaxy • 1.5k views

ADD COMMENT • link •

written 3.3 years ago by brian.hermann • 40

Hi Brian

"mismatching number of columns in header and data" is probably a clue, indicating that it is not a Galaxy problem but rather a data problem.

Could you please elaborate a little bit more, what you are actually doing? Are you using the "Get Data" -> "UCSC Main table browser" tool? And if so, what do you select?

Regards, Hans-Rudolf

ADD REPLY • link written 3.3 years ago by Hotz, Hans-Rudolf • 1.8k

Hi Hans-Rudolf,

Thanks for your reply - I noticed the mismatch column/header line, but I cannot understand how that can be the case, so I really appreciate your insights!

Yes, I am using get data from UCSC main table browser as below:

Click on Get Data in the upper part of left pane of Galaxy interface
Click on UCSC Main link
Set your genome and dataset of interest. It must be the same genome build against which you have mapped the reads contained in the BAM file you are analyzing
In the output format field choose selected fields from primary and related tables
Click get output button
In the first table presented at the top of the page select (using checkboxes) first 11 fields: name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinId
Click done with selection
Click Send query to Galaxy
A new dataset will appear in the current Galaxy history
Use this dataset as the input for Gene annotations in refFlat form dropdown of this tool.

When I do this for mm10, our galaxy instance, the ref Flat annotation is retrieved fine, but when I try hg19, it gives me the error noted above. Also, if I follow these steps in usegalaxy.org, the hg19 annotations from UCSC main table browser works fine, but when I try to import that file into my local galaxy instance, it doesn't work and I get essentially the same error. I would love to hear and suggestions.

Best,

Brian

ADD REPLY • link written 3.3 years ago by brian.hermann • 40

- what happens, when you download the 'successful' dataset from usegalaxy.org using the disk icon, and then try to upload the file into your local galaxy server?

- what happens if generate the same file directly in the UCSC table browser (not going via Galaxy) can you upload this file? is it different to the file you downloaded from usegalaxy.org?

ADD REPLY • link written 3.3 years ago by Hotz, Hans-Rudolf • 1.8k

If I do either of those things, download the successful dataset and upload it into local galaxy or download from UCUS table browser and upload into galaxy separately, I get essentially the same error:

Traceback (most recent call last):
  File "/var/local/galaxy-site/lib/galaxy/jobs/runners/local.py", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/var/local/galaxy-site/lib/galaxy/jobs/__init__.py", line 1200, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/var/local/galaxy-site/lib/galaxy/datatypes/tabular.py", line 919, in set_meta
    raise ('mismatching number of columns in header and data')
TypeError: exceptions must be old-style classes or derived from BaseException, not str

ADD REPLY • link written 3.3 years ago by brian.hermann • 40

So to summarize: the same tabular data is valid at usegalaxy.org, but cannot be uploaded to your local galaxy server causing the 'mismatching number of columns in header and data' error.

Apparently, usegalaxy.org is less stringent than your server - that's bizarre!

Do you mind sharing your history at usegalaxy.org with me (hrh@fmi.ch)?

Hans-Rudolf

ADD REPLY • link written 3.3 years ago by Hotz, Hans-Rudolf • 1.8k

Hi Hans-Rudolf - bizarre is precisely the word I used! Sure - happy to share a history - presumably from the local galaxy instance? The one I've been using locally is full of junk, so let me replicate this in a new history and get it in your hands.

-Brian

ADD REPLY • link written 3.3 years ago by brian.hermann • 40

And just to clarify - it DOES work with mouse annotations (mm10), just not human (hg19 or hg18) - very strange indeed!

ADD REPLY • link written 3.3 years ago by brian.hermann • 40

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