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CFSAN-Biostatistics / snp-pipeline

SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
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CLASSPATH is not configured with the path to Picard #11

Closed mshakya closed 6 years ago

mshakya commented 6 years ago

Hi. I am trying to run the pipeline, but keep getting this error despite adding Picard to the path (CLASSPATH) as suggested. Please help.

I have fulfilled all dependencies, and surprisingly Varscan works which is in the same directory as the picard.

Here is what my CLASSPATH looks like:

echo $CLASSPATH
/opt/apps/picard-tools-1.80/picard.jar:/opt/apps/picard-tools-1.80/VarScan.v2.3.9.jar:/opt/apps/picard-tools-1.80/picard-1.80.jar:/opt/apps/picard-tools-1.80/VarScan.v2.3.9.jar:/opt/apps/picard-tools-1.80/picard-1.80.jar:/opt/apps/picard-tools-1.80/VarScan.v2.3.9.jar:/opt/apps/picard-tools-1.8

Thanks

stevendavis commented 6 years ago

@mshakya Some things to try:

Step 1: Your CLASSPATH currently has Picard (and VarScan) listed multiple times.
/opt/apps/picard-tools-1.80/picard.jar /opt/apps/picard-tools-1.80/VarScan.v2.3.9.jar /opt/apps/picard-tools-1.80/picard-1.80.jar /opt/apps/picard-tools-1.80/VarScan.v2.3.9.jar /opt/apps/picard-tools-1.80/picard-1.80.jar /opt/apps/picard-tools-1.80/VarScan.v2.3.9.jar /opt/apps/picard-tools-1.8

Configure the CLASSPATH with only one picard jar file.

Step 2: Type this command at your command line: java picard.cmdline.PicardCommandLine This should not produce an error.

Step 3: If you still see errors, you could try a newer version of Picard.

mshakya commented 6 years ago

Thank you @stevendavis . I was using the older version, but i upgraded and now it works. however, i ran into another separate problem. I will open a separate issue for that. Thanks again.