Question: Fetch alignments using stitch Gene Blocks but all the gene-sequences are in '--------'
gravatar for yanghaobentley
3.0 years ago by
yanghaobentley0 wrote:

I was using the GALAXY project ( online server, the section is Fetch alignments -- > stitch Gene Blocks, and I wanted to extract some CDS genes in drosophila maf genome alignment file (from UCSC dm6 multiz27 way maf) according to a custom made BED file converted from GFF (the original file is from flybase dmel-all-r6.07.gff) file, however, as I do the extraction, the gene sequences I get are all in '-------'. As there is no genome build for dm6 in drosophila melanogaster, I build it myself via UCSC genome browser using the dm6 fasta genome sequences. Can anyone help me to sort out this problem? Thanks!

galaxy • 959 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by yanghaobentley0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


It is unclear how a custom reference genome (fasta format) would be used with this tool.

It might be best to send in a shared history link and we can examine the inputs and processing. Paste the link, the problematic dataset numbers, and a link to this post in an email to

Thanks, Jen, Galaxy Team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k

Thank you for sending in the details. The problem with executed failed job was due to a format issue with the MAF input (possibly an incomplete file load, but this could not be determined due to the dataset being permanently deleted). The problem with unexecuted jobs using a different MAF input is a mismatch between the chromosome identifiers in the MAF versus the BED input (these were deleted before the jobs completed, but would have failed or produced unexpected results).

General tool troubleshooting help: Support#Error_from_tools

Please correct the format errors and try the tool again. If there is an error, submit the problem as a bug report directly from the history leaving all inputs and the error dataset undeleted. (To confirm: fasta input is not needed when using this tool).

ADD REPLYlink written 3.0 years ago by Jennifer Hillman Jackson25k
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