Question: Abyss-pe Assembly error "terminate called after throwing an instance of 'std::bad_alloc'"
0
gravatar for 2kg2523
6.1 years ago by
2kg252310
Italy
2kg252310 wrote:

I am runnng 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?

ADD COMMENTlink modified 6.1 years ago by lelle830 • written 6.1 years ago by 2kg252310
1
gravatar for lelle
6.1 years ago by
lelle830
Berlin
lelle830 wrote:

'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.

ADD COMMENTlink written 6.1 years ago by lelle830
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