Warning in 1st line in SnpEff files

Question

[Rozita]

Hello,

I've got VCF files that I wish to annotate with SnpEff and then use SnpSift to add further annotations such as dbSNP, GWASCatalog, ClinVar, etc.

I run SnpEff by typing the following command

java -Xmx8g -jar snpEff.jar hg19 -chr -lof -hgvs -geneID -sequenceOntology -canon -csvStats sample_001.csv -stats sample_001.html input_001.vcf >sample_001_snpeff.vcf

When I type head sample_001_snpeff.vcf, I get the following sentence on the first line (which doesn't exist in the non-annotated input_001.vcf file):

[0.055s][warning][os,container] Duplicate cpuset controllers detected. Picking /sys/fs/cgroup/cpuset, skipping /dev/cpuset.

So when I run SnpSift dbSNP for instance of the SnpEff annotated file, I get the following error message:

VcfFileIterator.parseVcfLine(133):      Fatal error reading file 'sample_001_snpeff.vcf' (line: 1):
[0.055s][warning][os,container] Duplicate cpuset controllers detected. Picking /sys/fs/cgroup/cpuset, skipping /dev/cpuset.
Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
[0.055s][warning][os,container] Duplicate cpuset controllers detected. Picking /sys/fs/cgroup/cpuset, skipping /dev/cpuset.
        at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
        at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
        at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
        at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
        at org.snpsift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:77)
        at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:410)
        at org.snpsift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:397)
        at org.snpsift.SnpSift.run(SnpSift.java:580)
        at org.snpsift.SnpSift.main(SnpSift.java:76)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
[0.055s][warning][os,container] Duplicate cpuset controllers detected. Picking /sys/fs/cgroup/cpuset, skipping /dev/cpuset.
        at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1035)
        at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
        at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
        ... 8 more

I'm able to run SnpSift dbSNP on the non-annotated VCF files, which I can then merge with the SnpEff annotated files. But to run ClinVar for instance, I need to use the SnpEff annotated files and I'm still getting the same error message.

I'm not sure what exactly is wrong, could someone please assist me?

Thank you very much!

Answer 1

[Michael]

I was wondering why the warning goes to stdout not stderr. If it is really only the first line of the VCF file that is containing this warning you could remove the first line by piping the output through tail -n +2 (which will always remove the first line) or grep -ve "[warning][os,container]" (VCF files are not likely to contain this string anywhere).

Of course, the best way would be to make the cause for the warning disappear.

It might be possible that adding the java option: -Xlog:disable or -Xlog:all=warning:stderr:uptime,level,tags or a combination thereof could get rid of the warnings.

Googling the issue shows it is likely a bug of OpenJDK 16 that shows with certain configurations when running inside a Docker container: https://bugs.openjdk.org/browse/JDK-8270087 https://bugs.openjdk.org/browse/JDK-8293472 The solution is to update to a version of JDK that is not affected or not run inside a container.

[Rozita]

Thank you!

I did try tail -n +2 and then when I write that to a VCF file, I can use the subsequent tool. However, the output from the subsequent tool ends up having the same line being added to the new VCF file.

I'll look into updating OpenJDK then. Many thanks for your help.