error with samtools
0
0
Entering edit mode
5.8 years ago
mra8187 ▴ 20

dear all

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 ..?

RNA-Seq • 2.2k views
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3
Entering edit mode

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.

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2
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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.

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1
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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.

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0
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so how i can edit my script ?

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4
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First doing things step by step, if all parts work you can chain the commands using pipes.

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