This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Abyss-pe Assembly error "terminate called after throwing an instance of 'std::bad_alloc'"

I am running abyss-pe using two libraries on a server. After running for around 6 hrs, it gave me the following output (XXX and YYY represents the two libraries). I used k= 24

`XXX_R1.fastq': discarded 10 reads shorter than 24 bases
`XXX_R2.fastq': discarded 1639 reads shorter than 24 bases
`XXX_R2.fastq': discarded 50 reads containing non-ACGT characters
`YYY_R1.fastq': discarded 32 reads shorter than 24 bases

terminate called after throwing an instance of 'std::bad_alloc'

 what():  std::bad_alloc
make: * [OutPut-1.fa] Aborted (core dumped)

What did I go wrong? What shall I do to proceed with my assembly process?

abyss software-error next-gen assembly
• 7,660 views • link
updated by Ram Ram • written by 2kg2523 • 2kg2523

1 answer

'std::bad_alloc' generally means that the program could not allocate memory.

First thing I would check is, if there was enough free memory when the Abyss crashed.

• 1 views • link
updated by Ram Ram • written by lelle lelle

Log in to answer this question.

More posts like this