SINGHVJ-Bio
commented
2 years ago Looks like a GATK ASEReadCounter problem, so replaced following in modules.nf
gatk ASEReadCounter \ -R ${genome} \ -O ASE.tsv \ ${bam_params} \ -V ${vcf}
The new code added as ...
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 \ -jar /home/name/GenomeAnalysisTK-3.8/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar \ -T ASEReadCounter \ -R ${genome} \ -o ASE.tsv \ ${bam_params} \ -sites ${vcf}
The GenomeAnalysisTK.jar file downloaded from following link GenomeAnalysisTK.jar
@pditommaso, please check and update if ok
I am getting following error ..... Note: I verified input vcf file, and there are no duplicate SNPs observed. [July 7, 2022 7:40:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 4.55 minutes. Runtime.totalMemory()=2552233984
A USER ERROR has occurred: More then one variant context at position: chr3:10992891
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Using GATK jar /home/name/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/name/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar ASEReadCounter -R Homo_sapiens_assembly38_1-22_X.fasta -O ASE.tsv -I SAMPLE123XYZ.final.uniq.bam -V known_snps.vcf.gz