Likely missing parts highlighted in red. Try the command below:
Code:
USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | [COLOR="Red"]/[/COLOR]User/user/tan_analysis/samtools-0.1.19/bcftools[COLOR="Red"]/bcftools[/COLOR] view -bvcg - > eg2.raw.bcf
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