Question: MPileup output file error
gravatar for sfili
10 weeks ago by
sfili0 wrote:


I am running a bam file on MPileup, the running process takes more than a day, and then I get the following error: "Job output file grew too large (greater than 200.0 GB), please try different inputs or parameters". I don't know if this has to do anything, but I have enough enough space in Galaxy so this shouldn't be a problem.

Any suggestions?

Thank you.

size mpileup bam • 110 views
ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson25k • written 10 weeks ago by sfili0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


The memory (RAM) needed to execute tools is different than the memory allocated to store your account's data (quota).

You need to adjust what is being reported by the parameters set on the tool form, pre-filter the BAM to make it smaller (keep proper pairs, remove unmapped), or consider using your own Galaxy.

Problems with the inputs themselves can also trigger this type of error -- example: target custom genome is highly fragmented (1k or more reference sequences).

Please see:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 10 weeks ago by Jennifer Hillman Jackson25k
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