Closed PalmaGudiel closed 3 years ago
Hi @PalmaGudiel
Thank you for using our pipeline;
As I understand, the problem is in the path directory of raw files; in other words, you can't pass just the file path to the pipeline; you should create a folder for your raw files and then give that folder path to the pipeline. For instance, create a folder in /home/palmagudiel/rawFiles/ and copy all the fasta files into there; you should pass /home/palmagudiel/rawFiles/ to the pipeline.
Also, there is a video tutorial that might help to configure the pipeline.
Please let me know if you have any questions.
Hi @shahryary Thank your for your fast reply. I had already given the folder path to the pipeline (please see caption below).
I have also been checking the video tutorial for every step of the way, it's been useful to watch for other issues, just not for this particular one.
@PalmaGudiel thanks for your reply;
Could you please send me:
1- all the configuration parameters (from main menu --> 'C' --> number 10 "see configured parameters").
2- in linux bash please do ls -lah
and send just head of lists.
Thanks.
Yes, of course!
Please keep in mind that I am still at the beginning of the pipeline, I am aware that there might be several unresolved issues other than the problem with the raw files location/identification.
1) Configuration parameters:
Here is a summary of my current configuration parameters (it's a work in progress, right now I am focusing on being able to run at least the trimmomatic part):
2) ls -lah (you meant in the fastq folder with the raw files, right?)
Thanks again!
@PalmaGudiel thanks for sharing the configs.
I see the problem; the Pipeline reads all the files in zip format (usually trimmomatic use this format to improve performance), so all your files should be converted into fastq.gz
format. It's easy; you can do it with linux: go inside of the raw folder and run:
gzip *.fastq
.
It should zip all the files inside of the folder.
Now, you can re-config the path.
Also, I see you didn't configure the QC-Fastq path
if you need the report, you should configure this option too.
I knew for sure it was something dumb like this, sorry to have bothered you so much! It runs now, thank you very much!
Hi,
I found your MethylStar paper and pipeline while searching for straightforward methods for WGBS data preprocessing and I was particularly drawn to it since it is specifically mentioned that it is suitable for both experts and non-experts (I fall in the latter category). I am very used to work with R programming, but I am completely new to the ubuntu/bash environment so my question might be rather dumb!
While changing the configuration to set the proper paths to each requested file, I noticed that MethylStar is not recognizing my .fastq files, any idea why would that be? After specifying the corresponding path in the first step of the configuration "1. Path: RAW files" I get the following messages:
Founded 0 files in the directory.
Also, the size of your data-set almost: 4.8G
So, my 920 .fastq files do take up almost 4.8G but MethylStar does not seem to be recognizing the individual files as suitable input raw files.
I have tried running the first step of the pipeline (trimmomatic) but I get the following error messages: _Starting Trimmomatic ... Trimmomatic finished. Total time 0 Minutes. sort: cannot read: /home/palmagudiel/export_results/trimmomatic-files/list-finished.lst: No such file or directory rm: cannot remove '/home/palmagudiel/exportresults/trimmomatic-files/list-finished.lst': No such file or directory Something went wrong... something is going wrong... please run again.
But I don't really know if that's related to the "founded 0 files" issue or if it's completely unrelated.
Thank you very much in advance!!