Problem with downloading genome in SnpEff

Question

[Javier]

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

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted.

You used the double quote option, which mangled the code segment. Please edit your post and copy-paste the code segment again, and this time use the 101010 option to format the section properly.

[Javier]

Ok, sorry for that