vcf2genome error

[dbajpp0]

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)
[email protected], [email protected]

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

Command error:
VCF2Genome (v. 0.91 2017-01-13)
by Alexander Herbig (<= v0.84) and Alexander Peltzer (>v0.84)
[email protected], [email protected]

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:

1. Command line: nextflow run ...
2. 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

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:
• Image tag:

Additional context

[jfy133]

I'm very very sorry @dbajpp0 this completely slipped out of my TODO list

Unfortunately this appears to be an error with VCF2Genome.

I would suggest going into the working directory (if you still have the run /dades/jpp/data_WG_myotragus/eager/part1/work/5c/ab0ab35e55577260d159fd471ea82f) and send all the files there and the command eager is trying to execute ( 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) to the developer ([email protected]).

Altternatively you could try MultiVCFAnalyzer which serves the same purpose but with extra options