Bowtie2 for creating output(fastq) that are not aligned with reference

[zillur]

Hi there,
I tried to get the output from bowtie2 those reads which did not align. As Bowtie2 has the option on paired reads to spit out fastq files of things that fail to align concordantly (--un-conc <path>), and it has the option to spit out fastq files of things than align concordantly (--al-conc <path>).
I tried the following way:
Anyone can give me some idea???

Command: /home/zillur/Desktop/zillur/Tools/bowtie2-2.2.5/bowtie2-align-s --wrapper basic-0 -gbar 3 -x /home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti --passthrough -1 GI_7th_1.fastq -2 GI_7th_2.fastq
(ERR): bowtie2-align exited with value 1
[zillur@workstation01 Strain_GI]$ bowtie2 -x -gbar 3 /home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti -1 GI_7th_1.fastq -2 GI_7th_2.fastq --un-conc --al-conc
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LC_CTYPE = "UTF-8",
LANG = "en_US.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Warning: Output file '3' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Extra parameter(s) specified: "/home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti"
Note that if <mates> files are specified using -1/-2, a <singles> file cannot
also be specified. Please run bowtie separately for mates and singles.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/zillur/Desktop/zillur/Tools/bowtie2-2.2.5/bowtie2-align-s --wrapper basic-0 -x -gbar --passthrough -1 GI_7th_1.fastq -2 GI_7th_2.fastq 3 /home/zillur/Desktop/zillur/phd/Apecomplexan/B_microti/Reference/B_microti
(ERR): bowtie2-align exited with value 1

[SylvainL]

Hi,

I do not know so well bowtie2 but same kind of options exist for bowtie, and you have to give an output file for unmapped guys...

[zillur]

But how? Would you please to give me an example line.

[SylvainL]

--un-conc <output_file_un_conc> --al-conc <output_file_al_conc>

Reading the manual tells you that bowtie2 will automatically add .1 and .2 to each output_file to distinguish the mates...

[zillur]

Thank you very much for your kind reply. its working now.