-
Notifications
You must be signed in to change notification settings - Fork 1
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
Division by zero error? #2
Comments
Hi LeAnn, Thank you for using Prophage_Tracer. I think this error may be caused the command on line 81 in the prophage_tracer.sh script.
The purpose of this command is to estimate the insert_size of the DNA inserted fragment size of your constructed sequencing library. It is usually ~500 bp for paired-end libraries when resequencing bacterial genomes. Therefore, there may be a few situations caused this error.
Kaihao Tang |
Thank you for your quick response. I was using a single-end library, so I will try again will a paired end library and let you know if I have any further trouble. Thank you. |
I will update my script to be suitable for analysis of a single-end library. This is on my schedule. But if your analysis is very urgent, you can re-run using your single-end library data with reserving temporary files. In order to reserve temporary files, you should firstly delete the command on line 810 |
I tried running your Prophage_Tracer for the first time today and I got this error |
Hi, seharmaaz |
Hello WangLab-SCSIO, |
I have updated our codes and provided test data ( see README file). Please try to download the new shell scripts and the test data. Try to run on the test data. |
It should be noted that some users reported that blast+ 2.16.0 on Ubuntu may generate error and exit the shell script when using makeblastdb. However, this bulit DB is ok for downstream command. Therefore, I have updated the shell script to ignore this error message and continue with the following command. I also suggest to install blast+ 2.6.0 as mentioned in "System and software requirements". |
I tried running your Prophage_Tracer for the first time today and I got this error
awk: cmd. line:1: fatal: division by zero attempted
I followed your directions to index with bwa, then map with bwa then use samtools and everything worked up to this point in the script:
Do you have any test data that I can try to see if it is a problem with the input data?
Thank you
LeAnn
The text was updated successfully, but these errors were encountered: