CODEWITHSUNDEEP
shell
Hallo
Hallo

Reputation: 142

Shell script for loop error: Syntax error: word unexpected (expecting "do")

So I realize others have asked similar questions in the past, but when I tried their solutions (using dos2unix, and checking vim for extraneous symbols), they didn't work at all.

#!/bin/bash
#-----------------------------------------------------------------------------
mainDir=/mnt/data1/sam
#-----------------------------------------------------------------------------
----------------------------------------------------------------------------
#-----------------------------------------------------------------------------

#-----------------------------------------------------------------------------
cd $fastqDir
for i in `ls *R1_001.fastq.gz`
do
#----------------------------------
 filename="${i%_R1_001.fastq.gz}"
#---------------------------------- 
    #adapter-trim
#---------------------------------- 
 echo "Alignment started for $filename" >> ${qcDir}/${filename}_report.txt

 filename="${i%_R1_001.fastq.gz}"
 echo $filename

 echo "Alignment started for $filename" >> ${qcDir}/${filename}_report.txt
 sed '/chrM/d;/chrY/d;/random/d;/chrUn/d' < Aligned.out.sam | samtools view -bS -F 4 -q 30 -u - | samtools sort - > ${bamDir}/${filename}.bam 
 rm Aligned.out.sam
 mv Log.final.out ${qcDir}/${filename}_STARLogFinal.txt 

 echo "Picard started for $filename" >> ${qcDir}/${filename}_report.txt
 mv ${bamDir}/${filename}_dedup.bam ${bamDir}/${filename}.bam 
 samtools index ${bamDir}/${filename}.bam 

 echo "Picard insert size histogram for $filename" >> ${qcDir}/${filename}_report.txt
 INSERT_TXT_FILE="${qcDir}/${filename}.insertSizes.txt"
 INSERT_HISTO_FILE="${qcDir}/${filename}.insertSizes.pdf"

 echo "Making bigwig for $filename"
    lines=$(samtools view -c ${bamDir}/${filename}.bam);\
    bedtools genomecov -ibam ${bamDir}/${filename}.bam -bg -scale $(echo "1000000 / ${lines} " | bc -l) -g ${RefDir}/${genome}.chrom.sizes | \
    wigToBigWig -clip stdin ${RefDir}/${genome}.chrom.sizes ${bwDir}/${filename}.bw 2> $tmpDir/${filename}_log

 echo "macs2 for $filename"
done

I keep getting error 

Syntax error: word unexpected (expecting "do")

Sorry if this question is kind of silly, I'm completely new to shell scripting.

Upvotes: 0

Views: 965

Answers (1)

Hallo
Hallo

Reputation: 142

It turned out to be extraneous characters after all. I ran the following command and the script started working afterwards. Sorry for the confusion, and thanks for the help everyone!

tr -cd '\11\12\15\40-\176' < file-with-binary-chars > clean-file

Upvotes: 1

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