snpEff Error - Stop progressing after Predicting variants

Question

[woojoy14]

 snpEff -Xmx64g -v hg19 -s NA12878.Filtered.vcf > NA12878.Filtered.variants.ann.vcf

....

#       'Un_gl000235'   34474   Standard
#       'Un_gl000239'   33824   Standard
#       '21_gl000210_random'    27682   Standard
#       'Un_gl000231'   27386   Standard
#       'Un_gl000229'   19913   Standard
#       'M' 16571   Vertebrate_Mitochondrial
#       'Un_gl000226'   15008   Standard
#       '18_gl000207_random'    4262    Standard
#       'MT'    1   Vertebrate_Mitochondrial
#-----------------------------------------------

00:00:26    Predicting variants

I'm following the gatk best practice and when I used the code above, it stopped progressing after the Predicting variants and changed the status into sleeping mode.

When I checked the memory space, it was okay as below, I don't have an idea what is wrong with the code or data.

py27) [root@TSKimServer KW]# df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/sdb1       2.7T  433G  2.2T  17% /var2

How can I run the snpEff properly? I will really appreciate your help!

[Pierre Lindenbaum]

unless I'm wrong you're using a custom wrapper over snpEff . A Snpeff command looks like;

java -jar snpEff.jar -v -stats ex1.html GRCh37.75 protocols/ex1.vcf > protocols/ex1.ann.vcf

[WouterDeCoster]

Might be the result of an installation with conda

[pcsk9]

getting the same issue, what was the resolution?

[pcsk9]

update: the VCF path I provided had a typo in it,

SnpEff does not throw an error, it just hangs at "Predicting variants"