Question: FastQ to SAM conversion runs out of memory and fails
gravatar for yarmda
2.6 years ago by
yarmda0 wrote:

I'm trying to use the NGS Picard FASTQ to SAM conversion tool to start an RNA-Seq analysis. I am transferring FASTQ files from the EBI database, which offers the option to submit a job to Galaxy to pick up the files. This worked, but the conversion to SAM fails because the process uses more memory than was allocated.

How do you work around this?

rna-seq picard • 856 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by yarmda0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Given this error, the data is too large to process on the Main public Galaxy instance.

Section 2.8 of the Galaxy support wiki explains alternatives for working with data/jobs that exceed the compute resources at

Thanks for using Galaxy, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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