Marta Giovalli
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Activity overview
Latest activity by Marta Giovalli-
Marta Giovalli commented,
Updating to the latest version of GATK (4.2.6.1) did the trick. Thank you!
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Marta Giovalli commented,
Hi Genevieve, sorry for the late reply. The problem is that the docker container of the tool I need to execute is created with a read-only file-sys. Using the option --tmp-dir as you suggested did ...
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Marta Giovalli created a post,
Failure working with the tmp directory /tmp/
AnsweredHi, I've got this error but I do not understand the error since I do not ask for a tmp-dir. a) Using GATK jar /usr/bin/gatk-package-4.2.6.1-local.jar b) gatk --java-options -Xmx7g HaplotypeCaller ...
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Marta Giovalli created a post,
libgkl_compression.so not found + Failed to detect Google Compute Engine in a GATK workflow
AnsweredI have got a problem with the workflow "GATK Broad Best Practice Germline snps and indels variant calling 4.1.0.0" available here. It is a workflow using GATK IntervalListTools, HaplotypeCaller + M...