Error: Unable to access jarfile /picard.jar...
I face this problem in mark duplicate step as it was easily to release that i need to use this command in the tutorial to define the path
picard_path=$CONDA_PREFIX/share/picard-* ## 2.21.7-0
But also every time i change the directory i need to define it (just to be noted).
I face another error during sample indexing ...I decided not to use the for loop in the tutorial as i have only one file
Exception in thread "main" htsjdk.samtools.SAMException: Cannot write file: /home/ngs/workdir/Glaucomaproject/GATk/workdir/Glaucomaproject/GATk/SRR5858157.dedup.bai. Neither file nor parent directory exist.
http://broadinstitute.github.io/picard/command-line-overview.html#BuildBamIndex
I need to define out but file
java -jar picard.jar BamIndexStats
I=input.bam
O=output
They are dummy issues (:
Error: Unable to access jarfile /picard.jar...
I face this problem in mark duplicate step as it was easily to release that i need to use this command in the tutorial to define the path
picard_path=$CONDA_PREFIX/share/picard-* ## 2.21.7-0
But also every time i change the directory i need to define it (just to be noted).
I face another error during sample indexing ...I decided not to use the for loop in the tutorial as i have only one file
Exception in thread "main" htsjdk.samtools.SAMException: Cannot write file: /home/ngs/workdir/Glaucomaproject/GATk/workdir/Glaucomaproject/GATk/SRR5858157.dedup.bai. Neither file nor parent directory exist.
http://broadinstitute.github.io/picard/command-line-overview.html#BuildBamIndex
I need to define out but file
java -jar picard.jar BamIndexStats
I=input.bam
O=output
They are dummy issues (: