I got this while using RNA STAR:
EXITING because of fatal ERROR: not enough memory for BAM sorting:
SOLUTION: re-run STAR with at least --limitBAMsortRAM 6318500801
Jan 13 01:41:07 ...... FATAL ERROR, exiting
Is there any way around this or is it that the file is too large?
You can try to sort the file beforehand with “Samtools sort order of storing aligned sequences”. MAybe that helps. How big is your file?
Please also let us know which Galaxy server you are using
The paired end seqs are 14 and 11 GB each.
did you try to sort the BAM files before using STAR as @Flow suggested?
Did you get help for this already and solve the problem?
If not, this is one thing to check if I am understanding the problem correctly: An
RNA STAR job is failing during the last step in the processing (sorting the output
That can happen when there are a large number of target sequences (chromosomes, scaffolds, transcripts). Up to a hundred or so is fine, around a thousand can sometimes be Ok, but several hundred thousand or more (millions) won’t work. Why? The
Samtools sorting job will run out of memory.
If that is your use-case, the solution is to reduce the number of target sequences in the “custom genome”
fasta dataset or to use a different tool:
- If the
fasta is some transcript assembly that you created, check that you are removing very short sequences, especially those that would not be able to capture a hit anyway. The minimum length of the target sequences should be at around twice the length of the query sequences – and maybe a bit longer (~ 200 bases) – but you can generate the read lengths, filter the
fasta a few different ways, and test to see what works.
- If you are using a sequencing read dataset as a custom genome (ran
fasta or something similar), that will never work with
RNA-Star as far as I know and for a few different reasons both technical and scientific. Instead, use a tool like
BLAST, output a
tabular type of result (not a
BAM), and consider making the parameters very strict or the output can grow very very large for no practical purpose and potentially fail the job.
Just a guess and hopefully you’ve already resolved the error!