Failure working with the tmp directory /tmp/
Answered
Hi,
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 -I /var/extern/
geniosave/ERR3863191.100000.bam -R /var/extern/geniosave/chr2.fa.gz -O ERR3863191.100000.vcf
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async
_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx7g -jar /usr/bin/gatk-package-4.2.6.1-local.jar HaplotypeCaller -I /var/ext
ern/geniosave/ERR3863191.100000.bam -R /var/extern/geniosave/chr2.fa.gz -O ERR3863191.100000.vcf
c) A USER ERROR has occurred: Failure working with the tmp directory /tmp/. Try changing the tmp dir with with --t
mp-dir on the command line. Exact error was /tmp: Read-only file system
Thank you for any help you could provide
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Hi Marta Giovalli,
HaplotypeCaller by default uses temporary storage. You will need to specify a temporary directory that has read/write access. You can specify this directory with the option --tmp-dir (https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller#--tmp-dir).
Let me know if this works for you!
Best,
Genevieve
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Hi Marta,
We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!
Kind regards,
Genevieve
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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 the trick!
Thank you
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Great, thank you for posting the solution that worked!
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