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Issue with snpEff annotation - Process #546

Open aswani1208 opened 5 months ago

aswani1208 commented 5 months ago

Hi I am having issue while running snpEff for annotating the vcf file.The process is getting killed while running. What might be causing the issue?

Please see the error mentioned below

java -Xmx8g -jar snpEff.jar -v -stats ex1.html GRCh38.mane.1.2.refseq ~/variant_analysis/vcf/analysis_readychr20snps_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
davidhoover commented 5 months ago

Are you running out of memory? How large is your refseq file?