Question: snpEff killed while reading genome version
gravatar for j.lunger18
10 months ago by
j.lunger1810 wrote:

Hello, I'm trying to use snpEff to annotate a vcf file. There are not a lot of hints here, so I'm not sure why this is being killed...

   $ java -Xmx8g -jar $SNPEFF_JAR -c $SNPEFF_HOME/snpEff.config -v GRCh38.86 my.vcf > final.vcf
    00:00:00    SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
    00:00:00    Command: 'ann'
    00:00:00    Reading configuration file '/usr/local/apps/snpEff/4.3t/snpEff.config'. Genome: 'GRCh38.86'
    00:00:00    Reading config file: /usr/local/apps/snpEff/4.3t/snpEff.config
    00:00:00    done
    00:00:00    Reading database for genome version 'GRCh38.86' from file '/fdb/snpEff/4.3t/data/GRCh38.86/snpEffectPredictor.bin' (this might take a while)

Any help would be greatly appreciated. Thanks!

snp snpeff • 279 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 10 months ago by j.lunger1810

most likely is you are running out of memory, first check how much memory do you have, then try to increase the -Xmx8g parameter, that is only reserving 8GB RAM

ADD REPLYlink written 10 months ago by JC12k

Yep, I hadn't allocated enough memory. Thank you.

ADD REPLYlink written 9 months ago by j.lunger1810
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