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usegalaxy.* common tools
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Enhancement: Increase memory allocation to 18 GB for picard_MarkDuplicates3.1.1.0 at ORG #719

Open jennaj opened 4 months ago

jennaj commented 4 months ago

tool_id=toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0

The UseGalaxy.fr server is able to process the example job sent into bugs at ORG.

Job API ID bbd44e69cb8906b558621f8568c81354 (57015912)

jennaj commented 3 months ago

Update: Jetstream J2 is now allocated 12 GB instead of the default. This will address many of the prior failures.

submit_native_specification | --nodes=1 --ntasks=3 --mem=12288 --time=36:00:00 --partition=tpv

For anyone who still encounters jobs failing for memory resources, and who have confirmed there is not a data content or reference data issue (do check! you ask a question at our forum for community help), you will either need to reduce the BAM size (search the tool panel with filter bam and consider these options for scientific reasons too: an appropriate minimum mapQ, intact proper pairs, primary hits, exclude unmapped) or you can try at a different public Galaxy server -> UseGalaxy.eu or UseGalaxy.org.au are both good choices.

jennaj commented 1 week ago

Increased to 18 GB on August 28th.

If you had a recent failure at UseGalaxy.org, please try again now (including appropriate BAM filter strategies) before deciding to use a different server.