vcf2genome error - Githubissues

Dear Eager developer, I found an error on converting vcf file from GATK ug with vcf2geome. Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3280 at VCF2Genome.runUGAnalysis(VCF2Genome.java:284) at VCF2Genome.(VCF2Genome.java:148) at VCF2Genome.main(VCF2Genome.java:129) I send full error and nextflow log below. I also added info about OS, eager and nextflow as well as full command line input Could you pleae help me to sort it out? Thanks in advance, Joan

Check Documentation

I have checked the following places for your error:

[ x] nf-core website: troubleshooting
[x ] nf-core/eager pipeline documentation
- nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

Pipeline completed with errors- Error executing process > 'vcf2genome (50lib_myotragus_reads_clean_mapped)'

Caused by: Process vcf2genome (50lib_myotragus_reads_clean_mapped) terminated with an error exit status (1)

Command executed:

pigz -d -f -p 1 50lib_myotragus_reads_clean_mapped.unifiedgenotyper.vcf.gz vcf2genome -Xmx100g -draft 50lib_myotragus_reads_clean_mapped_UGVCFcsus.fasta -draftname "csusUG" -in 50lib_myotragus_reads_clean_mapped.unifiedgenotyper.vcf -minc 5 -minfreq 0.8 -minq 20 -ref Ovis_RNA_centroids95_part1.fa -refMod 50lib_myotragus_reads_clean_mapped_UGVCFcsus.fasta_refmod.fasta -uncertain 50lib_myotragus_reads_clean_mapped_UGVCFcsus.fasta_uncertainty.fasta pigz -f -p 1 50lib_myotragus_reads_clean_mapped_UGVCFcsus.fasta bgzip -@ 1 .vcf

Command exit status: 1

Command output: VCF2Genome (v. 0.91 2017-01-13) by Alexander Herbig (<= v0.84) and Alexander Peltzer (>v0.84) herbig@shh.mpg.de, peltzer@shh.mpg.de

Command error: VCF2Genome (v. 0.91 2017-01-13) by Alexander Herbig (<= v0.84) and Alexander Peltzer (>v0.84) herbig@shh.mpg.de, peltzer@shh.mpg.de

SNP statistics Quality Threshold: 20.0 Coverage Threshold: 5 Minimum SNP allele frequency: 0.8 sample SNP Calls coverage(fold) coverage(percent) refCall allPos noCall discardedRefCall discardedVarCall filteredVarCall unhandledGenotype Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 3280 at VCF2Genome.runUGAnalysis(VCF2Genome.java:284) at VCF2Genome.(VCF2Genome.java:148) at VCF2Genome.main(VCF2Genome.java:129)

Work dir: /dades/jpp/data_WG_myotragus/eager/part1/work/5c/ab0ab35e55577260d159fd471ea82f

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Steps to reproduce

Steps to reproduce the behaviour:

Command line: nextflow run ...
See error: Please provide your error message

Expected behaviour

Log files

Have you provided the following extra information/files:

[ ] The command used to run the pipeline
nextflow run nf-core/eager -profile docker -resume --fasta /dades/jpp/references/Ovis_RNA_centroids95_part1.fa --mapper bwamem --skip_fastqc --skip_adapterremoval --outdir /dades/jpp/data_WG_myotragus/eager/part1 --single_end --input /dades/jpp/data_WG_myotragus/clean_joan/mapped_reads/50lib_myotragus_reads_clean_mapped.fastq.gz --max_cpus 7 --max_memory 100.GB --max_time 500.h --run_vcf2genome true --vcf2genome_minc 5 --vcf2genome_minq 20 --vcf2genome_minfreq 0.8 --vcf2genome_header csusUG --vcf2genome_outfile UGVCFcsus --run_genotyping true --genotyping_tool ug --genotyping_source raw --gatk_call_conf 20 --gatk_ploidy 2 --gatk_ug_genotype_model SNP --gatk_ug_keep_realign_bam true --dedupper markduplicates --run_bam_filtering true --bam_unmapped_type discard --bam_mapping_quality_threshold 20 --gatk_ug_out_mode EMIT_ALL_SITES
[ ] The .nextflow.log file nextflow.log
[ ] The exact error:

System

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OS:
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Nextflow Installation

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Container engine

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nf-core / eager

vcf2genome error #1086