Bowtie2 align

Question

[saifulislam99121]

I am using bowtie2 to align . But after indexing, while I am running the bowtie2 , I am getting the following error. Can anyone help me? I need to know.

bowtie2 -x Baumannii_indexed.btindex -f -U M003786.fasta -s aligned.sam
stat: Bad file descriptor
Warning: Could not open read file "M003786.fasta" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1

[GenoMax]

Error says

Could not open read file "M003786.fasta" for reading

Is that file in the directory you are running this command from? What does head -3 M003786.fasta show?

[saifulislam99121]

Sorry. I have given the wrong file name. But when I have done everything ok, now this is the problem showing

bowtie2 -x Baumannii_indexed.fna -f -U M03786.fasta -s aligned.sam
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134

[Kevin Blighe]

Re-posted here: bowtie2