Question: Lastz hangs waiting to run
gravatar for kr81
3.3 years ago by
kr8110 wrote:

Hi all,

I have been trying to use Lastz to map an SRA dataset to a small FASTA file containing 16 amplicon sequences using the Galaxy main instance. I did a test analysis with one single amplicon sequence and the job ran to completion. When I start a job with the FASTA containing all 16 sequences, it hangs in the grey waiting to run mode for days and days, to the point where I am forced to delete it (I know deleting grey jobs is a no-no, but I didn't think that it would ever start running). I thought I might be able to get around this by using a cloud instance with the highest available RAM, but it appears that Lastz (any many of the other tools I use) are not available on the Cloudman version of Galaxy. Does anyone have any ideas about a work around?

Thanks :)

lastz galaxy cloudman • 765 views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by kr8110
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


For working on Main, double check these same factors (inputs, other queued jobs): Jobs stuck in limbo

Any tool in Tool Shed can be loaded into a Cloudman Galaxy. How-to is in the Galaxy wiki:

Hopefully one of these works out for you, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
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