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_4-kegg_4 centos:centos6 quay.io/biocontainers/bcftools:1.9--h68d8f2e_7
using singularity
+++ basename quay.io/biocontainers/bcftools:1.9--h68d8f2e_7
++ singularity pull --name bcftools:1.9--h68d8f2e_7 docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_7
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
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Copying blob sha256:dfda3e01f2b637b7b89adb401f2f763d592fcedd2937240e2eb3286fabce55f0

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Skipping fetch of repeat blob sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
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Copying blob sha256:10c3bb32200bdb5006b484c59b5f0c71b4dbab611d33fca816cd44f9f5ce9e3c

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Skipping fetch of repeat blob sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
Copying blob sha256:b89b6dc74fd44621b0404e04c1287b81d8dd9eb8f442e60225ca78a829e2c2e2

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Copying config sha256:50b61cb3d76c880d8cada7a96f0b7161298bf3fc4fc9ba30d4c6973dc35b5e96

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Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/user2/.singularity/cache/oci-tmp/8a102b1cdc6277cf16af18b7c37e3a109d68460744620ab1db2e992d85709383/bcftools_1.9--h68d8f2e_7.sif
+++ dirname quay.io/biocontainers/bcftools:1.9--h68d8f2e_7
++ mkdir -p /home/user2/img/quay.io/biocontainers
+++ basename quay.io/biocontainers/bcftools:1.9--h68d8f2e_7
+++ dirname quay.io/biocontainers/bcftools:1.9--h68d8f2e_7
++ mv bcftools:1.9--h68d8f2e_7 /home/user2/img/quay.io/biocontainers
++ set +ex
+ set -o pipefail
++ grep '[.]gz$'
++ echo input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ singularity exec -B /suikou/files/m64g/user2/work/yoshitake/129:/mnt --pwd /mnt /home/user2/img/biocontainers/samtools:v1.7.0_cv4 samtools faidx input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa
+ ref=input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa
+ bcftools call -vm -f GQ -o output.vcf
+ singularity exec -B /suikou/files/m64g/user2/work/yoshitake/129:/mnt --pwd /mnt /home/user2/img/quay.io/biocontainers/bcftools:1.9--h68d8f2e_7 bcftools mpileup -Ou --annotate AD,DP,INFO/AD -f input_2/Bomo_genome_assembly.minus.scaf034.scaf395.plus.NC_002355.re.fa input_1/SRR4425244_1.fastq.bam input_1/SRR4425245_1.fastq.bam input_1/SRR4425248_1.fastq.bam input_1/SRR4425249_1.fastq.bam input_1/SRR4425250_1.fastq.bam input_1/SRR4425251_1.fastq.bam
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 6 samples in 6 input files
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'singularity exec -B /suikou/files/m64g/user2/work/yoshitake/129:/mnt --pwd /mnt /home/user2/img/' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ echo 0
+ exit