i got an error message in bowtie2 run

Question

[carlosgonzalezcruz327]

Hi everyone, i'm new in bioinformatic and i have tried to run bowtie2 job. I want to use a fasta file like a query. I wrote the next command line:

./bowtie2 -x SLChr -f A11.fas -S ejempĺo.sam

but i got this error message:

terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) (ERR): bowtie2-align exited with value 134

i don't know what i did wrong and what the problem is.

the fasta file has scalffolds from a fungi specie. maybe the length of the sequence is the problem?

could someone help me?

[carlosgonzalezcruz327]

yes, that is what i want to do.

About you recommendation, after the last command line,i wrote this second one:

./bowtie2 -f -x SLChr -U 11A.fa -S salida.sam

but the message appeared up again.

Answer 1

[Trivas]

My guess is you're running into a memory usage issue. Can you share the command you used to build your SLChr index as well as some of your computer specs (e.g. ram and whether or not you are using a cluster)?

[carlosgonzalezcruz327]

this was my command: ./bowtie2-build Bchr_Fusarium.fasta SLCHr

My computer specs:

ram ---- 15.4 GiB

Intel® Core™ i7-10700 CPU @ 2.90GHz × 16

Mesa Intel® UHD Graphics 630 (CML GT2) internal storage----512.1 GB

I'm not using a cluster