Closed vnsriniv closed 6 years ago
This is quite weird, Varun. I will take a look into this.
Thanks! I used the Pro setup method. So the version in my computer is the github master.
It seems the error is too cryptic, and it simply is trying to say "the file is not there" :) With the previous commit, it will be clearer in the error message.
Basically, the pair_1
file is not here in your input_directory
:
/media/shared/Onedrive/Postdoc_Gu/Projects/Oligotyping_RockCreek/metagenomics/raw_fq/RC_AB4_062216-R1.fastq
Sorry!
Thanks Meren! Just as a follow up, would this issue arise because the file is a symbolic link? Because the file is there but it is a symbolic link.
Hmm. This is interesting. On my system it returns True for symlinks that exist and lead to a proper file, and returns False for symlinks that exist, but lead to a missing file.
What operating system are you using? Are you sure the symlink is working?
Hi Meren,
Thanks for your suggestion. It looks like my symbolic links were broken.. I fixed it and it works great now! Thanks again for your time and effort to help us clueless users! :)
Varun
Hi Meren,
I am getting this error when I perform
iu-merge-pairs
-Config File Error: Unexpected value for "pair_1" section "files": RC_AB4_062216-R1.fastq
. Not sure what the issue is. I prepared thesamples.txt
file (first two rows of the file shown below).I ran
iu-gen-configs
and then raniu-merge-pairs
as shown below (I also triediu-filter-minoche
to see if the issue was theiu-merge-pairs
command itself but that also gave the same error).Here is the appearance of the config file for the sample
Any help with this would be greatly appreciated! (I have this foreboding feeling that I am just missing something extremely obvious!).
Thanks Varun