snpEff killed while reading genome version

Question

[j.lunger18]

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!

[JC]

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

[j.lunger18]

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

[aswanikrishnap1994]

I have the same issue and even after allocating the memory still encountering same problem.

  java -Xmx8g -jar snpEff.jar -v -stats ex1.html GRCh38.mane.1.2.refseq ~/variant_analysis/vcf/analysis_rea
dychr20snps_filteredGT.vcf > ~/variant_analysis/annotation/filtered_snps.ann.vcf
00:00:00 SnpEff version SnpEff 5.2c (build 2024-04-09 12:24), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.mane.1.2.refseq'
00:00:00 Looking for config file: '/home/user/snpEff/snpEff.config'
00:00:00 Reading config file: /home/user/snpEff/snpEff.config
00:00:01 done
00:00:01 Reading database for genome version 'GRCh38.mane.1.2.refseq' from file '/home/user/snpEff/./data/GRCh38.mane.1.2.refseq/snpEffectPredictor.bin' (this might take a while)
00:00:06 done
00:00:06 Loading Motifs and PWMs
00:00:06 Building interval forest
Killed