biocontainers/samtools:v1.7.0_cv4 c2997108/centos7:1-trinity_2.8.5-kallisto_0.46.0-blast_2.9.0-trinotate-3.1.1-R_5-kegg_4 centos:centos6
using singularity
+ set -o pipefail
++ echo input_1/all.hiquality.100k.vcf
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
++ echo input_3/GCF_002163495.1_Omyk_1.0_genomic.fna
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ vcf=input_1/all.hiquality.100k.vcf
+ phenotype=input_2/phenotype.txt
+ ref=input_3/GCF_002163495.1_Omyk_1.0_genomic.fna
+ gq=20
+ dp=5
+ pval=1
+ corax=yes
+ th_snp=0.4
+ additional_chr=1000
+ set +o pipefail
++ grep -v '^##' input_1/all.hiquality.100k.vcf
++ head -n 2
++ tail -n 1
++ awk '-F\t' '{split($9,arr,":"); for(i in arr){if(arr[i]=="DP"){print i}}}'
+ pos_dp=3
++ grep -v '^##' input_1/all.hiquality.100k.vcf
++ head -n 2
++ tail -n 1
++ awk '-F\t' '{split($9,arr,":"); for(i in arr){if(arr[i]=="GQ"){print i}}}'
+ pos_gq=4
+ set +o pipefail
++ basename input_3/GCF_002163495.1_Omyk_1.0_genomic.fna
+ ln -s input_3/GCF_002163495.1_Omyk_1.0_genomic.fna input_1/all.hiquality.100k.vcf.GCF_002163495.1_Omyk_1.0_genomic.fna
++ basename input_3/GCF_002163495.1_Omyk_1.0_genomic.fna
+ ref=input_1/all.hiquality.100k.vcf.GCF_002163495.1_Omyk_1.0_genomic.fna
+ singularity exec -B /data/user2/work/yoshitake/106:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools faidx input_1/all.hiquality.100k.vcf.GCF_002163495.1_Omyk_1.0_genomic.fna
[E::fai_build3] Failed to open the FASTA file input_1/all.hiquality.100k.vcf.GCF_002163495.1_Omyk_1.0_genomic.fna
Could not build fai index input_1/all.hiquality.100k.vcf.GCF_002163495.1_Omyk_1.0_genomic.fna.fai
++ onerror 53
++ status=1
++ script=linkage-analysis~manhattan-plot
++ line=53
++ shift
++ set +x

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Error occured on linkage-analysis~manhattan-plot [Line 53]: Status 1

PID: 17993
User: user2
Current directory: /data/user2/work/yoshitake/106
Command line: linkage-analysis~manhattan-plot 
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