Melt.jar file cannot be accessed?
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
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Pierre Lindenbaum
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hgrsce •
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hgrsce •
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may be with a slash before ?
/home/user/scratch/MELTv2.2.2/MELT.jarI tried that, and that does not seem to be the issue.
so what is the output of
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.
Provide actual output of the commands @Pierre asked above.
Show us the lines in your script where you add the path with the forward slash.
The outputs are as follows:
and
you have to index the fasta with
samtools faidx /path/to/ref.fa