ebi-pf-team / interproscan

Genome-scale protein function classification
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File access error in test run #286

Closed Ghepardo closed 9 months ago

Ghepardo commented 2 years ago

Hi, I am running InterProScan 5.57-90.0 on an HPC cluster; I've installed it using EasyBuild. I am attempting to perform the test run described at https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html#interproscan-test-run. The test run does seem to complete, but in the process it produces the following error trace.

$ interproscan.sh -T . -i /home/apps/eb/software/InterProScan/5.57-90.0-GCCcore-11.2.0/test_all_appl.fasta -f tsv -dp
06/09/2022 10:12:13:706 Welcome to InterProScan-5.57-90.0
06/09/2022 10:12:13:707 Running InterProScan v5 in STANDALONE mode... on Linux
java.io.FileNotFoundException: /tmp/ed/./rothhpc413.cluster.local_20220906_101234410_22i3/kvstore/entryDB/LOCK (Permission denied)
        at java.base/java.io.RandomAccessFile.open0(Native Method)
        at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345)
        at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:259)
        at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:214)
        at org.iq80.leveldb.impl.DbLock.<init>(DbLock.java:45)
        at org.iq80.leveldb.impl.DbImpl.<init>(DbImpl.java:169)
        at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83)
        at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41)
        at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStoreEntry(Run.java:1757)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:465)
06/09/2022 10:12:35:967 RunID: rothhpc413.cluster.local_20220906_101234410_22i3
06/09/2022 10:13:02:412 Loading file /home/apps/eb/software/InterProScan/5.57-90.0-GCCcore-11.2.0/test_all_appl.fasta
...

The file referred to, and its parent directory, look like this:

$ ll -d /tmp/ed/./rothhpc413.cluster.local_20220906_101234410_22i3/kvstore/entryDB/ /tmp/ed/./rothhpc413.cluster.local_20220906_101234410_22i3/kvstore/entryDB/LOCK
drwxr-xr-x 2 eylese bis 4096 Jul 27 15:50 /tmp/ed/./rothhpc413.cluster.local_20220906_101234410_22i3/kvstore/entryDB/
-r--r--r-- 1 eylese bis    0 Jul 27 11:06 /tmp/ed/./rothhpc413.cluster.local_20220906_101234410_22i3/kvstore/entryDB/LOCK

I have tried this from both a directory on a remote filesystem mounted via NFS and on a local filesystem (/tmp, as in the output above), with the same result.

Here is my Java:

$ java --version
openjdk 11.0.2 2019-01-15
OpenJDK Runtime Environment 18.9 (build 11.0.2+9)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.2+9, mixed mode)

I have tried running this having set both export JAVA_TOOL_OPTIONS=-Djava.util.logging.ConsoleHandler.level=FINE and export JAVA_TOOL_OPTIONS=-Djava.util.logging.ConsoleHandler.level=DEBUG in turn, but these give no additional output.

Any idea what's going wrong here?