Skip to content

Error: Unable to access jarfile /picard.jar while indexing the sample for GATK #22

@SamahElmahdi

Description

@SamahElmahdi

while building bam index, this error shown.
this link was helpfull; http://seqanswers.com/forums/showthread.php?t=62872
i tried : java -Xmx2g -jar $picard_path/picard.jar BuildBamIndex VALIDATION_STRINGENCY=LENIENT INPUT=SRR5858162.dedup.bam # error
then i tried : java -Xmx2g -jar CONDA_PREFIX/share/picard-/picard.jar BuildBamIndex VALIDATION_STRINGENCY=LENIENT INPUT=SRR5858162.dedup.bam # the same error
then i tried to run this code again , picard_path=$CONDA_PREFIX/share/picard-
## 2.21.7-0
then the first code run correctly without error.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions