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  • Bash Error "Unexpected token near done"

    Hi!

    I wrote the following little bash script:
    Code:
    echo Processing...
    
    inputDir="/home/j490h/localhome/fastq/"
    output_folder="/home/j490h/localhome/fastq/textfiles/"
    
    for input_FASTQfile in `ls ${inputDir}/*fastq*`
    do
            filename_only=`basename ${input_FASTQfile}`
    	echo ${filename_only}
    	zcat ${filename_only} | sed -n '1~4p' > ${output_folder}/${filename_only}_ReadIDs.txt
    done
    
    output_folder2="/home/j490h/localhome/fastq/textfiles/combined_textfiles/"
    trimmed="trimmed"
    shuffled="shuffled"
    reconstructed="reconstructed"
    
    for file1 in `ls ${output_folder}/*txt*`
    do
    	for file2 in `ls ${output_folder}/*txt*` 
    	do
    		if [ ${trimmed} in ${file1} & ${file2} ]
    		then 
    			cat ${file1} ${file2} > ${output_folder2}/${file1}_${file2}_combined.txt
    		elif [ ${shuffled} in ${file1} & ${file2} ]
    		then
    			cat ${file1} ${file2} > ${output_folder2}/${file1}_${file2}_combined.txt
    		elif [ ${reconstructed} in ${file1} & ${file2} ]
    		then
    			cat ${file1} ${file2} > ${output_folder2}/${file1}_${file2}_combined.txt
    		else
    			echo Invalid input FASTQfile
    	done
    done
    and I get the error:
    "Unexpected token near done" at the last two lines.
    Unfortunately, I dont know why...
    I already checked cat -v file.sh, but there do not seem to be unexpected characters or something...

    Do you have any idea?

    Greetings!
    Last edited by GenoMax; 04-02-2019, 11:26 AM.

  • #2
    I believe you are missing a
    fi
    line before the last two done lines

    Comment

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