Melt.jar file cannot be accessed?

Question

[hgrsce]

Hi,

I know this might be very easy to fix, but I am quite new to this field. Basically I am trying to preprocess an alignment before I input it into MELT. I think there might be something wrong with java because once I try to submit the script, I am met with the following error:

Error: Unable to access jarfile home/user/scratch/MELTv2.2.2/MELT.jar

Edit:

if I put a forward slash in front of the path, so that it reads /home/user/scratch/MELTv2.2.2/MELT.jar I am met with the following error:

The full path to a reference genome AND .fai index is required!

Thank you in advance

[Pierre Lindenbaum]

may be with a slash before ? /home/user/scratch/MELTv2.2.2/MELT.jar

[hgrsce]

I tried that, and that does not seem to be the issue.

[Pierre Lindenbaum]

so what is the output of

ls -lah whatever/is/the/path/to/MELT.jar
file  whatever/is/the/path/to/MELT.jar

[hgrsce]

It just lists the file and file type, when there is a frwd slash, otherwise it cannot find the directory. However, when I put a frwd slash within the file where my script is, the path becomes unreadable. Without the frwrd slash before the full path in my script, I am just left with not being able to access MELT.jar.

[GenoMax]

Provide actual output of the commands @Pierre asked above.

[Ram]

Show us the lines in your script where you add the path with the forward slash.

[hgrsce]

The outputs are as follows:

/home/user/scratch/MELTv2.2.2/MELT.jar: Java archive data (JAR)

and

-rw-r-----+ 1 user user 8.3M Oct  5  2020 /home/user/scratch/MELTv2.2.2/MELT.jar

[Pierre Lindenbaum]

The full path to a reference genome AND .fai index is required!

you have to index the fasta with samtools faidx /path/to/ref.fa