Question: Custom Build reference WIDTH error
0
gravatar for jcolella.jc
3.0 years ago by
United States
jcolella.jc0 wrote:

Hello,

I am trying convert my data into gd format for use in the Convert tool under the Genomic Diversity tab. I have a filtered vcf file of all my SNPs already uploaded to Galaxy and was advised to "Custom Build" a reference genome using the reference I used for my original assembly. I have imported the reference .fna (fasta alternative) into Galaxy successfully and it shows up as a reference option when attempting to Convert the SNP file, but the conversion fails each time with this error:

Traceback (most recent call last):
File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/runners/__init__.py", line 590, in finish_job
job_state.job_wrapper.finish( stdout, stderr, exit_code )
File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/__init__.py", line 1232, in finish dataset.set_peek()
File "/galaxy-repl/instances/main/server/lib/galaxy/model/__init__.py", line 1633, in set_peek
return self.datatype.set_peek( self, is_multi_byte=is_multi_byte )
File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/miller
lab/genome_diversity/884ccb07885b/genome_diversity/lib/galaxy/datatypes/wsf.py", line 96, in set_peek

super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte, WIDTH='unlimited', skipchars=['#'] )
TypeError: set_peek() got an unexpected keyword argument 'WIDTH'

##I have previously  been able to use this tool without indicating a reference sequence but this no longer seems possible.

Any and all help greatly appreciated, thank you,

Jocelyn

 

 

ADD COMMENTlink modified 2.8 years ago by tiagoantao30 • written 3.0 years ago by jcolella.jc0
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Does the Custom Reference Genome/Build in fasta format have wrapped sequence lines? If not, please try doing this and re-running. Use the tool: Fasta manipulation > FASTA Width formatter

More about this type troubleshooting is explain in detail on the Galaxy wiki. In short, use strict fasta format to avoid format problems.
http://wiki.galaxyproject.org/Learn/CustomGenomes Section 8 Troubleshooting

Many tools have updated usage since around the beginning of the year and and prior workflows may require a bit of tuning to function as before. Backwards compatibility is always a priority, but sometimes this is not possible when there are significant changes (to tools or the underlying Galaxy code base). Changes will continue as Galaxy evolves.

Hopefully this resolves the issue, Jen, Galaxy team

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson25k

I ran the Fasta Manipulation tool on the custom built reference, but I still receive the same error when trying to convert my VCF file to a gd_SNP file. I have tried the width-corrected-Custom-Reference and an 'unspecified(?)' reference - all give the same error.

As an alternative I have transformed the VCF into pg_SNP using the Phentypic Association Tools, but there does not seem to be a pg_SNP to gd_SNP option in Galaxy? Though it looks like there were plans to add one ~2 years ago. Do you know of an available pg_SNP to gd_SNP script?

ADD REPLYlink written 2.9 years ago by jcolella.jc0
0
gravatar for tiagoantao
2.8 years ago by
tiagoantao30
United States
tiagoantao30 wrote:

The current genome diversity code seems to depend on the development version (on github) of galaxy. I had exactly the same problem on both usegalaxy and my own local server and solved it by running from the dev branch on my local server.

So, in practice, this code is broken on the main public server.

ADD COMMENTlink written 2.8 years ago by tiagoantao30

Thank you for the testing! A Trello ticket has been opened to track the problem and resolution: https://trello.com/c/ZBYLglM3

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k
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