I am using a program called Diamond and I have a command line that goes like this:

cd /srv/scratch/#/hello
diamond blastp -d /srv/scratch/#/goodbye/inputFile1.dmnd -q inputFile2.faa -o /diamond/outputFile.txt

I have my inputFile2.faa in the working directory (/srv/scratch/#/hello) and I have my other inputFile1.dmnd in another directory. As inputFile1.dmnd is a massive file and is being used in other command lines I do not want to move it to my current working directory as this would be impractical.

When I run this command line I get 'No such file or directory', is there a way to specify the absolute/relative path so I can keep my inputFile1.dmnd in a neutral directory?

I expect the answer to that question will help me with this one too but with my outputFile.txt I also want to specify which directory to put it in relative to my working directory, is there a way to do that?

The '#' in my paths are just my name on my university's server, just to hide my identity.

Thank you for reading and any help that may come!

I am using a program called Diamond and I have a script that goes like this:

cd /srv/scratch/*myname*/hello
diamond blastp -d /srv/scratch/*myname*/goodbye/inputFile1.dmnd -q inputFile2.faa -o /diamond/outputFile.txt

I have my inputFile2.faa in the working directory (/srv/scratch/myname/hello) and I have my other inputFile1.dmnd in another directory. As inputFile1.dmnd is a massive file and is being used in other command lines I do not want to move it to my current working directory as this would be impractical.

When I run this command line I get 'No such file or directory'.  Is there a way to specify the absolute/relative path so I can keep my inputFile1.dmnd in a neutral directory?

I expect the answer to that question will help me with this one too but with my outputFile.txt.  I also want to specify which directory to put it in relative to my working directory; is there a way to do that?

I am using a program called Diamond and I have a command line that goes like this:

cd /srv/scratch/#/hello
diamond blastp -d /srv/scratch/#/goodbye/inputFile1.dmnd -q inputFile2.faa -o /diamond/outputFile.txt

I have my inputFile2.faa in the working directory (/srv/scratch/#/hello) and I have my other inputFile1.dmnd in another directory. As inputFile1.dmnd is a massive file and is being used in other command lines I do not want to move it to my current working directory as this would be impractical.

When I run this command line I get 'No such file or directory', is there a way to specify the absolute/relative path so I can keep my inputFile1.dmnd in a neutral directory?

I expect the answer to that question will help me with this one too but with my outputFile.txt I also want to specify which directory to put it in relative to my working directory, is there a way to do that?

Thank you for reading and any help that may come!

I am using a program called Diamond and I have a command line that goes like this:

cd /srv/scratch/#/hello
diamond blastp -d /srv/scratch/#/goodbye/inputFile1.dmnd -q inputFile2.faa -o /diamond/outputFile.txt

I have my inputFile2.faa in the working directory (/srv/scratch/#/hello) and I have my other inputFile1.dmnd in another directory. As inputFile1.dmnd is a massive file and is being used in other command lines I do not want to move it to my current working directory as this would be impractical.

When I run this command line I get 'No such file or directory', is there a way to specify the absolute/relative path so I can keep my inputFile1.dmnd in a neutral directory?

I expect the answer to that question will help me with this one too but with my outputFile.txt I also want to specify which directory to put it in relative to my working directory, is there a way to do that?

The '#' in my paths are just my name on my university's server, just to hide my identity.

Thank you for reading and any help that may come!