Bowtie not accepting reads, help!

[thh32]

I am currently attempting to get Bowtie to map my reads onto an assembly using the following script

#$ -S /bin/sh
#$ -N bowtie_mapping_mccabe_abyss_original
#$ -M [email protected]
#$ -q large.q
#$ -cwd

module load bowtie/2.1.0

bowtie2 -q -x /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/Original_Assemblies_Mapped/Abyss/McCabe_metavelvet_index {-1 McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_
NoIndex_L002_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhur
st-SAB_NoIndex_L006_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R1_001_qualtrim.trimmed5P.fastq.oneline.matched -2 McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-Ric
hardDewhurst-LAB_NoIndex_L002_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-g
DNA-RichardDewhurst-SAB_NoIndex_L006_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R2_001_qualtrim.trimmed5P.fastq.oneline.matched } -S /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/Original_Assembli
es_Mapped/Abyss/Abyss_Original_bowtie.sam

As my files are fastq I used the -q option, -x states the prefix to my index files, then all 12 of my read files are entered via -1 and -2 to identify the read 1 and read 2 files and -s states the name of the output SAM file.

I have left the {} around the read files as it was in the manual and as when I remove that I get an error stating no read files have been entered and to use with -u/-1/-2, however when I submit this file I get an error file stating

Error: 1 mate files/sequences were specified with -1, but 0
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/bowtie/2.1.0/bowtie2-align --wrapper basic-0 -q -x /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/Original_Assemblies_Mapped/Abyss/McCabe_metavelvet_index -S /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files
_.fastq/Original_Assemblies_Mapped/Abyss/Abyss_Original_bowtie.sam -1 -2 {-1 McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gD
NA-RichardDewhurst-LAB_NoIndex_L003_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L006_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,Mc
Cabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R1_001_qualtrim.trimmed5P.fastq.oneline.matched } McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R2_001_qualtrim.trimmed5P.fastq.oneline.m
atched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L006_R2_001_qualtrim.trimmed5P.fastq.on
eline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R2_001_qualtrim.trimmed5P.fastq.oneline.matched
bowtie2-align exited with value 1

I have previously used bowtie to separate out the reads that map to a assembly with those that don't and that worked absolutely fine and all read files were accepted so I can't understand what is wrong now. Any help would be greatly appreciated.

Thanks

[thh32]

Now appears to be working although its exactually the same as a script I tried earlier.

#$ -S /bin/sh
#$ -N bowtie_mapping_mccabe_abyss_original
#$ -M [email protected]
#$ -q large.q
#$ -cwd

module load bowtie/2.1.0

bowtie2 -q -x /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/Original_Assemblies_Mapped/Abyss/McCabe_metavelvet_index -1 McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L006_R1_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R1_001_qualtrim.trimmed5P.fastq.oneline.matched -2 McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L001_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L002_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-LAB_NoIndex_L003_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L004_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L006_R2_001_qualtrim.trimmed5P.fastq.oneline.matched,McCabe-gDNA-RichardDewhurst-SAB_NoIndex_L007_R2_001_qualtrim.trimmed5P.fastq.oneline.matched  -S /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/Original_Assemblies_Mapped/Abyss/Abyss_Original_bowtie.sam