Open EldeVries opened 3 years ago
Hi, are you running the example data ? if not, could you run the example to see if it works or not ?
Hi, Thanks for the reply! Yeah I've run both the data set and my own set of data and the "cat: write error: Broken pipe" message is consistent across both.
It looks strange. What is the whole command you run the tool ?
Hopefully you can read the command there.
The command is correct. Could you please run this command in your output directory ? cat ./iter*/contig.*.fa | perl -ne 'if (/^>/){print ">r$.\n";}else{print;}' >corrected.fa
Does this code work, is this file corrected.fa
empty ?
The code runs but corrected.fa isn't empty.
I cannot reproduce this error. It is probably due to using a different system. Maybe you could try on a different machine, or use bash /abspath/to/strainline.sh
rather than /abspath/to/strainline.sh
Hi, That's really odd that its not reproducible. It might be the machine. I can give it a shot and let you know. Using the bash command doesn't change the outcome at all.
Hi, I am encountering this error when I try to use trimmed reads. If the reads aren't trimmed they work fine; any ideas why this occurs?
Hi, so this command already works for the example dataset on your machine?
Hey all!
I have also experienced this error when running the test dataset.
cat: write error : Broken Pipe
I am curious this issue has been resolved!
Thanks! Peter
Hi Xiao,
I've been attempting to run your Strainline program- however, I consistently encounter this error which states "Broke pipe". Not sure what this is referring too but I have attached an image.
Thanks!
Ellen![Capture1](https://user-images.githubusercontent.com/81272056/127094639-7fa12b53-066a-48ca-8c0e-83e1a48b838d.JPG)