Issue with config file for quality filtering

[vnsriniv]

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 the samples.txt file (first two rows of the file shown below).

sample	r1	r2
RC_AB4_062216	RC_AB4_062216-R1.fastq	RC_AB4_062216-R2.fastq

I ran iu-gen-configs and then ran iu-merge-pairs as shown below (I also tried iu-filter-minoche to see if the issue was the iu-merge-pairs command itself but that also gave the same error).

iu-gen-configs samples.txt -o 01_QC
iu-merge-pairs --debug 01_QC/RC_AB4_062216.ini 

Config File Error: Unexpected value for "pair_1" section "files": RC_AB4_062216-R1.fastq

Here is the appearance of the config file for the sample

[general]
project_name = RC_AB4_062216
researcher_email = u@example.edu
input_directory = /media/shared/Onedrive/Postdoc_Gu/Projects/Oligotyping_RockCreek/metagenomics/raw_fq
output_directory = /media/shared/Onedrive/Postdoc_Gu/Projects/Oligotyping_RockCreek/metagenomics/01_QC

[files]
pair_1 = RC_AB4_062216-R1.fastq
pair_2 = RC_AB4_062216-R2.fastq

Any help with this would be greatly appreciated! (I have this foreboding feeling that I am just missing something extremely obvious!).

Thanks Varun

[meren]

This is quite weird, Varun. I will take a look into this.

[vnsriniv]

Thanks! I used the Pro setup method. So the version in my computer is the github master.

[meren]

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!

[vnsriniv]

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.

[meren]

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?

[vnsriniv]

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