gravatar for stefan

4 hours ago by

Maastricht University, NL

I am a bachelor student (biomedical sciences). We are doing a Illumina sequencing task to find out a subjects heritage.
Currently, I am struggling with our alignment step and I can't manage to find the answer anywhere.
This is my code:

bowtie2 --threads 10  -x Reference/Bowtie2/homosapiens  -1 trimOutput/lc_good_1.fastq  -2 trimOutput/lc_good_2.fastq -S  > alignmentOutput/lc.bowtie.sam

And the error messages:

 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: /cm/shared/apps/bowtie2/2.4.2/bin/../src/bowtie2-2.4.2/bowtie2-align-s --wrapper basic-0 --threads 10 -x Reference/Bowtie2/homosapiens -S -1 -2 trimOutput/lc_good_2.fastq trimOutput/lc_good_1.fastq
(ERR): bowtie2-align exited with value 1

I have read the bowtie2 -help page a hunder times but can't seem to find the solution. Any help is much appreciated!

This is the first time I'm working with a programming language so use simple words in your response 🙂

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modified 4 hours ago


GenoMax ♦ 97k


4 hours ago

stefan • 0

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