Bowtie Parameter Switch Error

Bowtie Parameter Switch Error

1

I’m having this problem when running bowtie2 and can not figure it out. I am running a fairly basic bowtie2 command shown here

bowtie2 –very-sensitive -x
/usr/lusers/achits/achits/genomes/Xtropicalis9/Xtropicalis9 -1
z1.fastq -2 z2.fastq -X 2000 -p 14 -S

and for some reason the error I’m getting is showing my command switched up. I’ll show you what I mean. Here is the error:

Error: 0 mate files/sequences were specified with -1, but 1 mate
files/sequences were specified with -2. The same number of mate
files/ sequences must be specified with -1 and -2. Error: Encountered
internal Bowtie 2 exception (#1)

Command: /home/achits/bin/tools/bowtie2-align-s –wrapper basic-0
–very-sensitive -x /usr/lusers/achits/achits/genomes/Xtropicalis9/Xtropicalis9 -X 2000 -p
14 -S -1 -2 z2.fastq z1.fastq
(ERR): bowtie2-align exited with value1

Looking closely (bold parts of above) what I notice is that for some reason bowtie2 is switching up my parameters so that the bowtie2 command doesn’t have my first file under the -1 parameter. It moves that file to the end of the command. Anyone know what the problem could be?


bowtie2


alignment

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