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Old 10-26-2017, 07:54 AM   #1
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 51
Default Bowtie2 input read error

Hi All

Bowtie2 is not able to recognize my paired end data input. Seems to be a command line related error but I checked the fastqs anyway and both appear to be fine and properly paired. Note the rendering of the command line in the error. Any idea whats wrong?



$  /usr/local/thirdparty/bowtie2/bowtie2-2.1.0/bowtie2 --no-mixed --no-discordant --no-dovetail --no-contain --sensitive-local -I 151 -X 700 -x dataset_18153.dat  -1 A9_S1_L001_R1_001_val_1.10000.10000.fq -2 A9_S1_L001_R2_001_val_2.10000.10000.fq -S -1509026240-bowtie2.sam

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: /usr/local/thirdparty/bowtie2/bowtie2-2.1.0/bowtie2-align --wrapper basic-0 --no-mixed --no-discordant --no-dovetail --no-contain --sensitive-local -I 151 -X 700 -x dataset_18153.dat -S -1 -2 A9_S1_L001_R2_001_val_2.10000.10000.fq A9_S1_L001_R1_001_val_1.10000.10000.fq,509026240-bowtie2.sam
bowtie2-align exited with value 1
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Old 10-26-2017, 08:05 AM   #2
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 51

Nevermind, I spotted it. This command-line, which was generated programmatically, contains the following erroneous argument.

-S -1509026240-bowtie2.sam

The hypen in "-1509026240-bowtie2.sam" is the culprit.

Thanks anyway

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bowtie2 error mate pairs

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