Error in job variant_calling
Dear, while running MT pipeline, I got the following error:
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 ANALYSIS
1 PLATYPUS
1 assembly_contig_length
1 call_contig_depth
1 call_gene_depth
1 fastqc_raw
1 krona
1 metaquast
1 rename_stat_output
1 variant_calling
1 visualize
1 vizbin
12
rule variant_calling:
input: Assembly/mt.assembly.merged.fa, Assembly/mt.reads.sorted.bam, Assembly/mt.assembly.merged.fa.fai, Assembly/mt.reads.sorted.bam.bai
output: Analysis/mt.variants.samtools.vcf.gz
jobid: 7
wildcards: type=mt
echo "[x] mt VARIANT CALLING `date +"%Y/%m/%d %H:%M:%S"`"
#temporary directory and files
VCF_MPU=$(mktemp --tmpdir=/tmpdata -t "XXXXXX.mpu.vcf")
echo "$VCF_MPU"
### run_mpileup Assembly/mt.assembly.merged.fa Assembly/mt.reads.sorted.bam Analysis/mt.variants.samtools.vcf.gz
echo "Running samtools mpileup"
samtools mpileup -uAf Assembly/mt.assembly.merged.fa Assembly/mt.reads.sorted.bam | bcftools view -vcg - | vcf-convert -r Assembly/mt.assembly.merged.fa -v 4.2 > $VCF_MPU
bgzip -c $VCF_MPU > Analysis/mt.variants.samtools.vcf.gz
tabix -f -p vcf Analysis/mt.variants.samtools.vcf.gz
[x] mt VARIANT CALLING 2020/05/17 11:04:29
/tmpdata/AMRNfR.mpu.vcf
Running samtools mpileup
bash: line 11: vcf-convert: command not found
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported
Failed to open -: could not parse header
Error in job variant_calling while creating output file Analysis/mt.variants.samtools.vcf.gz.
RuleException:
CalledProcessError in line 37 of /scratch/gencore/ma5877_test_software/meta_trans/imp/IMP/rules/Analysis/variant.rule:
Command '
echo "[x] mt VARIANT CALLING `date +"%Y/%m/%d %H:%M:%S"`"
#temporary directory and files
VCF_MPU=$(mktemp --tmpdir=/tmpdata -t "XXXXXX.mpu.vcf")
echo "$VCF_MPU"
### run_mpileup Assembly/mt.assembly.merged.fa Assembly/mt.reads.sorted.bam Analysis/mt.variants.samtools.vcf.gz
echo "Running samtools mpileup"
samtools mpileup -uAf Assembly/mt.assembly.merged.fa Assembly/mt.reads.sorted.bam | bcftools view -vcg - | vcf-convert -r Assembly/mt.assembly.merged.fa -v 4.2 > $VCF_MPU
bgzip -c $VCF_MPU > Analysis/mt.variants.samtools.vcf.gz
tabix -f -p vcf Analysis/mt.variants.samtools.vcf.gz
' returned non-zero exit status 127
File "/scratch/gencore/ma5877_test_software/meta_trans/imp/IMP/rules/Analysis/variant.rule", line 37, in __rule_variant_calling
File "/scratch/gencore/conda3/envs/imp_env/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message```[mt.assembly.merged.fa.fai](/uploads/2035dfa3b5be4e8161c3dc96a68dfec3/mt.assembly.merged.fa.fai)
[mt.assembly.merged.fa](/uploads/81af5c316d3e6cb28b6c7f0ec5af2e43/mt.assembly.merged.fa)
[mt.reads.sorted.bam.bai](/uploads/5aaecd857cac427c7efde0d9850ceb06/mt.reads.sorted.bam.bai)