Question: MPileup output file error
0
gravatar for sfili
8 weeks ago by
sfili0
sfili0 wrote:

Hi,

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 • 85 views
ADD COMMENTlink modified 8 weeks ago by Jennifer Hillman Jackson25k • written 8 weeks ago by sfili0
1
gravatar for Jennifer Hillman Jackson
8 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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: https://galaxyproject.org/support/#troubleshooting

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 weeks ago by Jennifer Hillman Jackson25k
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