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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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New release of picard #13

Closed EnzoAndree closed 5 years ago

EnzoAndree commented 6 years ago

Hello,

I would like to point out that with the new picard (2.18.10) snp-pipeline raises an error:

CLASSPATH is not configured with the path to Picard

Although the CLASSPATH is well configured, beacuse just installing the previous version (2.18.9) everything goes smoothly.

It is not a big deal but the error message is't very informative.

Greetings

stevendavis commented 6 years ago

This is fixed in the new version 2.0.0 released today.

bifidoman commented 6 years ago

Hi

I installed snp_pipeline and picard today and I get the same error

bifidoman commented 6 years ago

Hi

I even get this error when installing Picard 2.18.9 and when changing the .conf file to "removeduplicatereads=False" any help is appreciated

stevendavis commented 6 years ago

@bifidoman Please reach out to me directly. You can find my email address in my github profile. Send me the full path to your picard.jar file and send me the contents of your CLASSPATH environment variable. echo $CLASSPATH

Meanwhile, there is a workaround. With the release of cfsan snp pipeline version 2.0.0, Picard is used in two parts of the workflow, removing duplicate reads and during local realignment around indels. As a workaround, you could disable both of these steps in the configuration file.

RemoveDuplicateReads=false EnableLocalRealignment=false

stevendavis commented 6 years ago

Fixed in release 2.0.1 today. My apologies for the delay. EDIT: you will need release 2.0.2 if running Python 3.