AlexanderDilthey
commented
1 year ago Hi @shawez,
You can add the parameter customGraphDir to specify a custom graph files search directory.
You still specify --graph, i.e. your full call may e.g. look like this: ./HLA-LA.pl --BAM /home/shawez/HLA-LA/rawData/sample1.recal.bam --graph PRG_MHC_GRCh38_withIMGT --customGraphDir /path/to/graph/dir --sampleID sample1 --workingDir /home/shawez/HLA-LA/outPut
When using this command, HLA*LA will expect to find the graph files in /path/to/graph/dir/PRG_MHC_GRCh38_withIMGT.
Best wishes
Alex
Hello,
I recently started using HLA-LA which is installed on the cluster of my institute.
I also downloaded an additional data package as per the instructions from the developers. Then I run the following line of code to index the graph locally.
/services/tools/hla-la/1.0.3/opt/hla-la/bin/HLA-LA --action prepareGraph --PRG_graph_dir /home/shawez/HLA-LA/graphs/PRG_MHC_GRCh38_withIMGT
Now, I am trying to run HLA-LA on my one sample using a BAM file.
My code is
cd /services/tools/hla-la/1.0.3/bin ./HLA-LA.pl --BAM /home/shawez/HLA-LA/rawData/sample1.recal.bam --graph PRG_MHC_GRCh38_withIMGT --sampleID sample1 --workingDir /home/shawez/HLA-LA/outPut
I am getting the following error:
Graph directory /services/tools/hla-la/1.0.3/opt/hla-la/src/../graphs/home/shawez/HLA LA/graphs/PRG_MHC_GRCh38_withIMGT not found - valid graph names are subdirectories of the graphs directory in the HLA-LA root at ./HLA-LA.pl line 247.
I tried to change the path of the graph but did not work.
Is there any other possible solution you can suggest for this issue?
Thank you very much.
Best,
Shawez