Question: snpEff killed while reading genome version
0
gravatar for j.lunger18
10 months ago by
j.lunger1810
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)
    Killed

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
2

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 961 users visited in the last hour
_