I'm trying to align numerous fastq files to the hg19 reference with bowtie2. I have a shell script that should read in the fastq files (paired end) and align them to their reference as per the script laid out in bowtie's instruction manual.
executing this script returns this error:
I've even tried to remove the -2 file and run as a -U alignment, which returns a similar error message:
Any technical support is appreciated!
Thanks
Code:
#cd /home/psychgene/Documents/bowtie bowtie2 -x hg19 -q -1 $/media/psychgene/My\ Passport/RNA-Seq\ FASTQ/ERR188028_1.fastq -2 $/media/psychgene/My\ Passport/RNA-Seq\ FASTQ/ERR188028_2.fastq -S ERR188028.sam
Code:
Warning: Same mate file "$/media/psychgene/My" appears as argument to both -1 and -2 Extra parameter(s) specified: "Passport/RNA-Seq", "FASTQ/ERR188028_1.fastq", "Passport/RNA-Seq", "FASTQ/ERR188028_2.fastq" 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: /usr/bin/bowtie2-align --wrapper basic-0 -q -x hg19 -S ERR188028.sam -1 $/media/psychgene/My -2 $/media/psychgene/My Passport/RNA-Seq FASTQ/ERR188028_1.fastq Passport/RNA-Seq FASTQ/ERR188028_2.fastq bowtie2-align exited with value 1 psychgene@psychgene-VirtualBox:~/Documents/bowtie$ sh FASTQ.sh Warning: Same mate file "$/media/psychgene/My" appears as argument to both -1 and -2 Extra parameter(s) specified: "Passport/RNA-Seq", "FASTQ/ERR188028_1.fastq", "Passport/RNA-Seq", "FASTQ/ERR188028_2.fastq" 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: /usr/bin/bowtie2-align --wrapper basic-0 -x hg19 -q -S ERR188028.sam -1 $/media/psychgene/My -2 $/media/psychgene/My Passport/RNA-Seq FASTQ/ERR188028_1.fastq Passport/RNA-Seq FASTQ/ERR188028_2.fastq bowtie2-align exited with value 1
Code:
Warning: Same mate file "$/media/psychgene/My" appears as argument to both -1 and -2 Extra parameter(s) specified: "Passport/RNA-Seq", "FASTQ/ERR188028_1.fastq", "Passport/RNA-Seq", "FASTQ/ERR188028_2.fastq" 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: /usr/bin/bowtie2-align --wrapper basic-0 -x hg19 -q -S ERR188028.sam -1 $/media/psychgene/My -2 $/media/psychgene/My Passport/RNA-Seq FASTQ/ERR188028_1.fastq Passport/RNA-Seq FASTQ/ERR188028_2.fastq bowtie2-align exited with value 1 psychgene@psychgene-VirtualBox:~/Documents/bowtie$ sh FASTQ.sh Extra parameter(s) specified: "Passport/RNA-Seq", "FASTQ/ERR188028_1.fastq" Error: Encountered internal Bowtie 2 exception (#1) Command: /usr/bin/bowtie2-align --wrapper basic-0 -x hg19 -q -S ERR188028.sam -U $/media/psychgene/My Passport/RNA-Seq FASTQ/ERR188028_1.fastq bowtie2-align exited with value 1
Thanks
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