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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?

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    What is the full error message? – Kusalananda May 25 '19 at 6:59
  • diamond v0.9.24.125 | by Benjamin Buchfink <buchfink@gmail.com> Licensed under the GNU GPL <gnu.org/licenses/gpl.txt> Check github.com/bbuchfink/diamond for updates. #CPU threads: 16 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) No such file or directory – gwrathe May 25 '19 at 7:10
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    Is both the files /srv/scratch/myname/goodbye/inputFile1.dmnd, /srv/scratch/myname/hello/inputFile2.faa, and the directory /diamond available (are you able to ls them)? Are you running this as a job on a cluster with something like Slurm? If so, are the file and directory available on the compute node running the job? – Kusalananda May 25 '19 at 7:16
  • Are you sure the error is not about inputFile2.faa? – Rui F Ribeiro May 25 '19 at 7:18
  • Yep, I can ls both. Yes, it is being run on a cluster with a job scheduler. The files and directories are no less available than any others like the directory I cd'd to. I thought I might have simply not known how to do this but it looks like it's shaping up to be something I might talk to our HPC IT people about. – gwrathe May 25 '19 at 7:26
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Assuming these are the real paths, the problem is most likely the character #.

Options:

1) Don't use # in file or directories names, if you can avoid it. So rename /srv/scratch/# to something else, like /srv/scratch/hash. You'll need escaping (see below) to do this.

2) Escape # with a backslash:

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

3) Escape the complete filename with single quotes:

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

You can test all this by using a standard command like ls together with the filename, and optional bash tab completion (which will add escaping).

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    bash (for example) would have no issue with # when specified as part of a pathname like what the user is doing. – Kusalananda May 25 '19 at 7:01
  • I am using bash. I'm terribly sorry, I should have clarified, the # is just my name on my university's computer that I replaced to hide my identity. – gwrathe May 25 '19 at 7:12

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