This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Running GenomicsDBImport: stuck on 'INFO GenomicsDBImport - Importing batch 1 with 62 samples'
I am running GenomicsDBImport on 62 human exome data and somehow the process stuck in the very beginning of the process. Please see below message:
16:24:19.150 INFO ProgressMeter - Starting traversal 16:24:19.150 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute 16:24:19.378 INFO GenomicsDBImport - Starting batch input file preload 16:24:36.900 INFO GenomicsDBImport - Finished batch preload 16:24:36.900 INFO GenomicsDBImport - Importing batch 1 with 62 samples
It stucks right here for several hours.
Here is the command I used:
java -jar $GATK GenomicsDBImport -R $hg19 \ --sampleNameMap sample.map -L chr1 \ --genomicsdb-workspace-path $output
I wonder if this is normal. Thank you for your help in advance!