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
FastqReader Error? #1
Comments
Can you please report the first 4 lines of your |
EDIT: The name of the file originally was |
Weird. Your snippet of the FASTQ file looks identical to the ones I have been assembling. What is your operating system? If you are okay with sharing your data, I can try a larger snippet (~100 lines) of your read files. You can send me a link of the read file(s) to my email: kmnip@bcgsc.ca |
Just as a sanity check, I've tried running RNAbloom using the older java version as specified in the README. So far, the program is running well. Below is the version I am using :
I'll give an update when the program finishes. |
Thanks for the sanity check! The code was compiled with Java 8, but I tested with Java 10 before. I actually expect a different part of the code would break in Java 11... |
I am able to replicate the |
I have figured out what the issue is! |
This bug is fixed in release v1.1.1. Thanks for reporting this bug! |
Right. I was waiting for the program to finish, but otherwise I think it's running fine (I think I have to re run with the increased heap size). Cheers. |
fix bug in edge-filtering and overlap-sorting by start position
I am trying to run RNA-Bloom for Nanopore cDNA sequencing reads, but it seems like it is failing....
Below is the message I am getting if I run the program with an input fastq (uncompressed) file.
Below is the message I am getting if I run the program with an input bgzip compressed fastq file. It runs for some time and then it dies. There's bunch of intermediary files.
Below are the args :
args: [-ntcard, -c, 3, -k, 17, -indel, 10, -e, 3, -p, 0.8, -long, sample.fastq, -t, 16, -outdir, .]
Below is the java version :
I've tried with different cDNA samples (all Nanopore) but they all give the same error.
The text was updated successfully, but these errors were encountered: