This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Malloc_error_break and job termination while running Kallisto

Good morning, all,

I'm running Kallisto on a Mac (OX X El Capitan 10.11.6) and I think I am getting a memory error while running Kallisto quant. Unfortunately, my computer skills aren't such that I can work around the issue on my own.

My Kallisto Index ran without any issue, producing a file of transcripts.idx file of 177 mb in size (FASTA file obtained from Patcher Lab Kallisto website). The .fastq.gz files are 400 mb each. I have pasted the entry/error I receive while running Kallisto Quant below. Has anyone else received this error while attempting to run Kallisto? Does anyone know of a good workaround? Thanks in advance!

$ kallisto quant -i transcripts.idx -o output -b 100 2_S1_L001_R1_001.fastq.gz 2_S1_L001_R2_001.fastq.gz
[quant] fragment length distribution will be estimated from the data 
[index] k-mer length: 31 [index] number of targets: 88,198 
[index] number of k-mers: 82,099,631 
[index] number of equivalence classes: 0 <P>kallisto(2237,0x7fff7656b000) malloc: *** mach_vm_map(size=281469558853632) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc 
Abort trap: 6
rna-seq kallisto memory
• 2,761 views • link
written by MagnumOpus • MagnumOpus

How much memory do you have on this Mac? Do you get the error right away or after some time?

• 1 views • link
written by GenoMax GenoMax

4gb x2.

I tried clearing out memory hogging apps (Chrome, etc.). Memory used hovers around 4gb, cached files approx 2.5 gb, no swap used.

• 1 views • link
written by MagnumOpus • MagnumOpus

1 answer

Update/resolved: the memory error resolved after three cycles of shutting down. Not skilled enough to explain why, but happy I'm finally able to run Kallisto Quant without error. Perhaps another program I was running was causing a memory leak.

Thanks for the help genomax!

• 1 views • link
written by MagnumOpus • MagnumOpus

Log in to answer this question.

More posts like this