-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
The Path Issue #3
Comments
Hi, it should be path of the directory.... if fasta path DB/HUMAN_RNA/rRNA.fasta You should mention this in the following way (for configuration file) RIBO_DB=DB/HUMAN_RNA Let me know, if it doesn't solve your issue. |
Thank you for your reply! Actually, I strictly follow the User Guide.pdf for setting up the config file. Wrong filepath or input file not existent: /home/kc/workspace/output/INTERMEDIATE_FILES/RIBO/unmapped_1_RIBO_UNALIGNED.fasta. And I check the RIBO folder, It's really empty there. It means that there is anything to be written in this folder. bash ./decontaMiner.sh -i /home/kc/workspace/fasta/data_test/website_examples -o /home/kc/workspace/output -c /home/kc/decontaMiner_1.4/config_files/configure.txt -- WELCOME TO THE DECONTAMINER PIPELINE -- INFO: input file format (-f) not specified. BAM assumed
EXTERNAL SOFTWARE HUMAN RIBOSOMAL/MITOCHONDRIAL DNA CONTAMINATING ORGANISMS DATABASES
[opt_ref:194] ERROR: The file /home/kc/workspace/fasta/Human_rna/rRNA.fasta,/home/kc/workspace/fasta/Human_rna/rRNA.idx is not an existing/valid absolute or relative path
done. Output written in /home/kc/workspace/output/INTERMEDIATE_FILES/RIBO/unmapped_1_RIBO_UNALIGNED |
Are you using 'test_data.tar.gz' as an input? Here I am sharing the configuration file that I have tested recently ..
|
Hi, thank you for providing your configure.txt for reference. According to your configure.txt, I found that the version of the software tools I use is different from yours. So I reinstalled all the software tools to your version. It works now. |
That's great. |
Hi,
I met a problem when I ran decontaMiner.sh. I just use your original databases and data(download from https://www-labgtp.na.icar.cnr.it/decontaminer/), but it said" ./Human_rna/rRNA.fasta, Human_rna/rRNA.idx is not an existing/valid absolute or relative path. I have checked the configure.txt, that's all right. Could you help me to solve the problem? Thank you so much!
The text was updated successfully, but these errors were encountered: