Running Rockhopper from a command-line

Question

[langziv]

Hi

I'm attempting to run the the program with a command that's in the following structure:

java -Xmx1200m -cp Rockhopper.jar Rockhopper -g genome/path 1.fastq%2.fastq,3.fastq%4.fastq 5.fastq%6.fastq,7.fastq%8.fastq

The command is written according to the program's instructions. When running the command the following error message in printed:

Error: Could not find or load main class Rockhopper

When running java -Xmx1200m -cp Rockhopper.jar Rockhopper the program's instructions are printed, so I don't understand why this error occurs.

I'd love to get some ideas on how to resolve the issue.

[Pierre Lindenbaum]

the program's instructions are printed

what are those instruction please.

and what is the output of

jar tvf Rockhopper.jar  | grep -F Rockhopper.class

[langziv]

I managed to resolve the issue by passing absolute paths instead of relative ones.
Now I'm trying to solve the fact that I got multiple ptt and rnt files, because I'm working with an assembly with contigs rather than a genome.

[Ram]

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Answer 1

[langziv]

I managed to resolve the issue by passing absolute paths instead of relative ones.