GATK Funcotator [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)

[CromitDolores0808]

Bug Report

18:47:11.757 INFO Funcotator - Shutting down engine
[September 19, 2021 6:47:11 PM CST] org.broadinstitute.hellbender.tools
.funcotator.Funcotator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1885339648
org.broadinstitute.hellbender.exceptions.GATKException: Unable to query
the database for geneName: WASH7P
....
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.ins
tanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.ins
tanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Mai
n.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: org.sqlite.SQLiteException: [SQLITE_IOERR_LOCK] I/O error i
n the advisory file locking logic (disk I/O error)
at org.sqlite.core.DB.newSQLException(DB.java:909)

Affected version(s)

GATK 4.1.9.0

Description

GATK Funcotator [SQLITE_IOERR_LOCK] I/O error in the advisory file locking logic (disk I/O error)

I downloaded the data-sources by "gsutil cp gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200521s.tar.gz .". I can't find useful information for this error. Thank you.

Steps to reproduce

Using GATK jar /lustre1/ruibinxi_pkuhpc/ljx/software/gatk-4.1.9.0/gatk-
package-4.1.9.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_i
o_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjd
k.compression_level=2 -jar /lustre1/ruibinxi_pkuhpc/ljx/software/gatk-4
.1.9.0/gatk-package-4.1.9.0-local.jar Funcotator -R /home/ruibinxi_pkuh
pc/lustre1/ljx/reference_genomes/hg38_bwa/hg38.fa -V /home/ruibinxi_pku
hpc/lustre1/ljx/data/raodn/WES/GATK/P14P_filtered.vcf.gz -O /home/ruibi
nxi_pkuhpc/lustre1/ljx/data/raodn/WES/GATK/P14P_filtered_funcotator.maf
--output-file-format MAF --data-sources-path /home/ruibinxi_pkuhpc/lus
tre1/ljx/reference_genomes/funcotator_dataSources.v1.7.20200521s/ --ref
-version hg38

[jonn-smith]

I believe this is an issue with the lustre filesystem (it doesn't seem to support locking). Others have reported this kind of issue with sqlite as well (CGATOxford/CGATPipelines#39).

Unfortunately, I'm not aware of any way to fix the issue itself while using lustre.

However, you can move the funcotator data sources to a local disk and it should work fine.