Entering edit mode
6.3 years ago
mra8187 ▴ 20
i have some problem with samtools ....
samtools mpileup -u -q 10 -f '/media/mra/4A3B44B64CA65A93/SNP/DATA/Genom/refrense_genome/Apis_mellifera.GCA_000002195.1.dna.chromosome_group.1.fa' '/media/mra/4A3B44B64CA65A93/SNP/DATA/drone-larvae/SRR1571717/segemehl/f-sort.bam' | bcftools view -g - | vcfutils.pl varFilter | awk '($6 >= 50)' > '/media/mra/4A3B44B64CA65A93/SNP/DATA/drone-larvae/SRR1571717/segemehl/file.raw.pileup' [E::hts_open_format] fail to open file '' [mpileup] failed to open : No such file or directory : command not found : command not found : command not found
what's my script problem ..?
Unless you know how each component works, avoid pipes because those will just confuse you. Based on a quick look (while preparing food) it looks like quite a number of things in your command are wrong.
I am trying to format the content OP posted but the content is confusing both the website and me - what I see above is not what is being shown when I hit edit.
Then let's wait for OP to clarify. But looking at the error messages I get the idea OP is piping things into "empty" commands.
so how i can edit my script ?
First doing things step by step, if all parts work you can chain the commands using pipes.