snpEff Error - Stop progressing after Predicting variants
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!
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pcsk9 •
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woojoy14 •
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woojoy14 •
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unless I'm wrong you're using a custom wrapper over snpEff . A Snpeff command looks like;
Might be the result of an installation with conda
getting the same issue, what was the resolution?
update: the VCF path I provided had a typo in it,
SnpEff does not throw an error, it just hangs at "Predicting variants"