Bowtie Parameter Switch Error

Question

[datascientist28]

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?

[datascientist28]

UPDATE: I have figured out a way to make bowtie2 run and that's by specifying a sam file for output (-S). My thought from the bowtie2 manual is that -S without an option prints to the standard out, anyone know why this isn't happening????

[GenoMax]

If you omit -S altogether then the output goes to stdout.

[saarantras]

This should be filed as a bug report. Very odd.

Answer 1

[datascientist28]

Thank you genomax2. "If you omit -S altogether then the output goes to stdout." taking out the -S fixed the problem