Hi, I'm trying to annotate some VCF files, but when I attempt to run the annotation process, I encounter three errors: two related to "too many symbolic links" and one related to "not finding the genome". I tried running one of the test exposed in the web using different versions (GRCh38.105 and GRCh37.75), but I encountered the same error. Additionally, when I try to use java -jar snpEff.jar download
, it gives the first two errors.
SnpEff version: 5.2
SnpEff full command line: java -Xmx8g -jar snpEff.jar GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf Error message:
java.lang.RuntimeException: java.io.IOException: Too many levels of symbolic links
at org.snpeff.util.Download.unzip(Download.java:374)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:41)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:61)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:110)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1212)
at org.snpeff.SnpEff.loadDb(SnpEff.java:514)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:884)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:869)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by:java.io.IOException: Too many levels of symbolic links
at java.base/java.io.UnixFileSystem.canonicalize0(Native Method)
at java.base/java.io.UnixFileSystem.canonicalize(UnixFileSystem.java:175)
at java.base/java.io.File.getCanonicalPath(File.java:626)
at org.snpeff.util.Download.unzip(Download.java:342) ... 10 more
java.lang.RuntimeException: Genome download failed!
at org.snpeff.SnpEff.loadDb(SnpEff.java:515)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:884)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:869)
at org.snpeff.SnpEff.run(SnpEff.java:1173) enter code here
at org.snpeff.SnpEff.main(SnpEff.java:163)
Update: i solve it, the data directory was a symbolic link instead of an actual dir. so i just delate it and now everything works
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