I have a bash script like below. First it will take sorted.bam files as input and use “stringtie” tool give each sample gtf as output. Then path for each sample gtf will be given into mergelist.txt. and then use “stringtie merge” on them to get “stringtie_merged.gtf”.
I totally have 40 sorted.bam files.
for sample in /path/*.sorted.bam
do
dir="/pathto/hisat2_output"
dir2="/pathto/folder"
base=`basename $sample '.sorted.bam'`
"stringtie -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/${base}/${base}_GRCh38.gtf -l ${dir2}/stringtie_output/${base}/${base} ${dir}/${base}.sorted.bam; ls ${dir2}/stringtie_output/*/*_GRCh38.gtf > mergelist.txt; stringtie --merge -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/stringtie_merged.gtf mergelist.txt"
done
I separated the commands with ; After running the script on all sorted.bam files and after completing the job I see that mergelist.txt has paths only for 33 sample gtf’s. Which means the path for other 7 sample gtfs is missing in merge list.txt.
Is Separating the commands with ; right one or is there any other way?
The script should use one command first and with the output the paths need to be given in the text file and then use the other command.
Advertisement
Answer
You haven’t separated the commands with semi-colons; you’ve invoked a single command that has semi-colons embedded in it. Consider the simple script:
"ls; pwd"
This script does not call ls followed by pwd. Instead, the shell will search the PATH looking for a file named ls; pwd (that is, a file with a semi-colon and a space in its name), probably not find one and respond with an error message. You need to remove the double quotes.