Broken pipe error

[EldeVries]

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

[HaploKit]

Hi, are you running the example data ? if not, could you run the example to see if it works or not ?

[EldeVries]

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.

[HaploKit]

It looks strange. What is the whole command you run the tool ?

[EldeVries]

Hopefully you can read the command there.

[HaploKit]

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 ?

[EldeVries]

The code runs but corrected.fa isn't empty.

[HaploKit]

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

[EldeVries]

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.

[EldeVries]

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?

[HaploKit]

Hi, so this command already works for the example dataset on your machine?

[fermpeter]

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