rmhubley
Cannot Read File
I am trying to softmask a fungal genome and get the following error:
When I use ls to look in my directory, it says that the fasta file (Polycephalomyces_Cleaned.fasta) is there.
I am very new to programming and have no idea what might be wrong. Thanks in advance.
Can you show the output of ls -l /home/brittany/Aaron/RepeatMasker/Polycephalomyces_Cleaned.fasta?
It looks like you are using only Dfam. Dfam does not include any fungal-specific repeats, so the masking will likely be incomplete. You will get better masking if you install RepBase RepeatMasker Edition (requires a subscription), or if you use and/or create a curated library of repeats from that organism or a closely related one.
Thank you for such a quick response! Here is the output after I did ls -l :
Also, thank you for the suggestion about the fungal-specific repeats. I'm not sure how to make the library of repeats but will look into it!
I will add that after I ran this code there now is a Fungal library: /RepeatMasker/Libraries/CONS-Dfam_3.1/Fungi that contains 9 fungal-specific repeats.
That is very unusual: the Polycephalomyces_Cleaned.fasta file is not readable or writable by anyone. Running the command chmod 0644 Polycephalomyces_Cleaned.fasta will reset it to a sane default, and after that RepeatMasker should be happy to run on it. However, the library issue is worse than I realized:
I will add that after I ran this code there now is a Fungal library: /RepeatMasker/Libraries/CONS-Dfam_3.1/Fungi that contains 9 fungal-specific repeats.
Unfortunately those 9 repeats are used to recognize clonal artifacts and are not actually fungi-specific. In fact, Dfam only includes repeats from Metazoa and descendants.
That worked and the file can now run! How would you suggest fixing the library problem? Making a custom library of fungal repeats and running -lib?
I see that RepBase has a library of fungal repeats, but the subscription is almost $1500. Do you have any other suggestions of where I could find a good database? Thank you for all your help!
I am wondering the same thing as above. I have used tantan to mask repeats because I am not sure of a better database for fungi. Any suggestions?
