CFSAN-Biostatistics/snp-pipeline

CLASSPATH is not configured with the path to Picard

mshakya opened this issue · 2 comments

mshakya commented

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

@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

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.