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STAR on Galaxy
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15 months ago


I have been having issues trying to implement an RNA-seq pipeline through Galaxy using an AWS cloud instance. My goal is to start from raw reads and get to gene counts. However, I have been having issues getting STAR to run. My current error is

Fatal error: Matched on fatal error
EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc
Possible cause 1: not enough RAM. Check if you have enough RAM 32002674832 bytes
Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v 32002674832
Jun 03 21:16:00 ...... FATAL ERROR, exiting

I don't believe this is a memory issue as my current cloud instance is using a .xlarge image and the cloudman console says I have used 43G of my total 100G of data. My input datasets are a pair of paired end reads, loaded as fastq.gz. I have also loaded USCS GR38 gene annotation to be used and match the built in reference genome hg38 (which is from USCS I believe.

My STAR input is

-paired-end as individual datasets.
-use built in index
    -use genome reference without builtin gene-model
    -Human (Homo sapiens) (b38): hg38
    -Gene model: UCSC_GR38_annotation.gtf
-length of genomic sequence around annotated junctions: 49

(read lengths were 50)

any help would be appreciated

RNA-Seq • 166 views
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Memory is not storage. How much RAM do you have available in your instance? STAR is kinda known to need a lot of that.

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If you are really sure you have the necessary amount of RAM available, did you try the proposed solution?

SOLUTION: run ulimit -v 32002674832

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hi jmgoldstein7,

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

Entering edit mode
15 months ago

The m5.xlarge instance that I am using has 16 GB of memory. And from the line

Check if you have enough RAM 32002674832 bytes

Which equates to 32 GB I think you are right and I was mixing up memory and storage like an amateur! Thank you, and for the tip about readability. For future reference, if I were to try the proposed solution, on Galaxy it is obviously a little different, is the section

Maximum available RAM (in bytes) for sorting
If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced. (--limitBAMsortRAM)

The right section to change to the memory limit? Thanks again


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