Error when try to run ./rattle
Kirovez opened this issue · 6 comments
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
Hi Ilya,
how large is the file, and how much memory available do you have?
Hi,
I have 512Gb RAM and 1 Tb free disk space. My fastq has only 300,000 reads.
Ilya
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
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.
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!