Melt.jar file cannot be accessed?
0
0
Entering edit mode
12 weeks ago
hgrsce • 0

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

Java MELT • 475 views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

so what is the output of

ls -lah whatever/is/the/path/to/MELT.jar
file  whatever/is/the/path/to/MELT.jar
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Provide actual output of the commands @Pierre asked above.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1616 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6