Abyss-pe Assembly error "terminate called after throwing an instance of 'std::bad_alloc'"
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6.7 years ago
2kg2523 ▴ 10

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?

Assembly software error next-gen • 6.1k views
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Entering edit mode
6.7 years ago
lelle ▴ 830

'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.

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