Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error when try to run ./rattle #17

Open
Kirovez opened this issue Aug 5, 2020 · 6 comments
Open

Error when try to run ./rattle #17

Kirovez opened this issue Aug 5, 2020 · 6 comments

Comments

@Kirovez
Copy link

Kirovez commented Aug 5, 2020

Hi!
I try to run RATTLE with my fastq reads (direct RNA sequencing):
./rattle cluster -i my.fastq -t 24 --fastq --iso --rna -r 5

I got an error:

what(): cannot create std::vector larger than max_size()
RNA mode: 1 Reading fasta file... Done terminate called after throwing an instance of 'std::length_error' Aborted (core dumped)

Can you help with this, please?

Ilya

@novikk
Copy link
Collaborator

novikk commented Aug 5, 2020

Hi Ilya,

how large is the file, and how much memory available do you have?

@Kirovez
Copy link
Author

Kirovez commented Aug 6, 2020

Hi,
I have 512Gb RAM and 1 Tb free disk space. My fastq has only 300,000 reads.

Ilya

@novikk
Copy link
Collaborator

novikk commented Aug 6, 2020

And what is the size of the largest read? Is it possible for you to send me the fastq via email so that I can check what's going on?

Thanks

@Kirovez
Copy link
Author

Kirovez commented Aug 13, 2020

I tried to tun with different datasets and this error ('Segmentation fault (core dumped)') always occurred. The reads I used are publically available and can be downloaded via this link: https://sra-pub-src-2.s3.amazonaws.com/ERR3764351/col0_nanopore_drs_4.tar.gz.1 / I hope it will help in debugging.

@EduEyras
Copy link
Member

EduEyras commented Aug 13, 2020 via email

@novikk
Copy link
Collaborator

novikk commented Aug 13, 2020

Hi @Kirovez

I've checked the files you provided and I've found the problem. The issue is that these files were basecalled on windows, so there is an extra character before the line end (line ends in windows are \r\n while they are only \n in unix).

I will try to push a fix so that RATTLE accepts files basecalled in Windows ASAP, but meanwhile you can fix the line endings with the following command:

sed 's/\r//g' file.fq > file.fixed.fq
Tell me if that worked for you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants