Hi I'm very new to this script thing, so please be gentle.
I am trying to get a command - the mach2qtl command in the code below - to loop through a set of files.
Each command should take the same two .dat and .ped files, but the .mlinfo and .mlprob files with filenames including 'chrom1' should be run together and output to a file PC_full_1.txt
I have run the command fine by retyping it using the appropriate file names, but would like to run this as a script that runs through files 1 - 22.
When I run the script below I get a segmentational error.
What am I doing wrong?
Thanks,
Polly
Code:
#! /bin/bash
# program to run through each chromosome carrying out association using mach2qtl
# increment through chromosome numbers
i=0
while [ $i -lt 23 ]
do
i=$(( $i +1 ))
#list info and prob files 1 - 22
infofile=chrom$i_step2.mlinfo
probfile=chrom$i_step2.mlprob
# run mach2qtl using the above specified files
mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile > PC_full_$i.txt
done
exit 0
The error message "segmentation fault" comes directly from the OS. Somehow it tries to execute the program "mach2qtl" and this program crashes. This is definitely not a problem coming out of your script, at least not directly.
A little hint: if you have a loop which behaves strangely try to "echo" out all the commands in question. This way you will see (instead of execute) what is to be execute:
Code:
i=0
while [ $i -lt 10 ] ; do
command_in_question someparameter $i some_more_param
(( i += 1 ))
done
Modify this to:
Code:
i=0
while [ $i -lt 10 ] ; do
echo command_in_question someparameter $i some_more_param
(( i += 1 ))
done
to see if what you think is executed is really executed. In loops more complicated than this example this can widely differ.
Another possibility is to insert "set -xv" at the start of the loop and "set +xv" at the end. This sends every line as it is interpreted to stderr. ("set -xv" turns this on, "set +xv" turns it off). You can monitor the script as it is executed like this:
Code:
script param1 param2 .... 2>&1 1>/dev/null | more
Lets talk about your script itself now:
Code:
infofile=chrom$i_step2.mlinfo
While not directly incorrect this could be misleading to the shell: suppose you have two variables, "$i" and "$i_". How should the shell find out which one you mean? If you want to expand a variable in the middle of a string write it this way:
Code:
infofile=chrom${i}_step2.mlinfo
This will remove all ambiguity. Further, make it a habit to ALWAYS QUOTE your strings, because a misplaced (or unexpected) space character could well lead to disaster, because it is a separator to the shell. Therefore always write
Code:
infofile="chrom${i}_step2.mlinfo"
and similarly for the other line in your script.
Btw., it seems that your variables "$infofile" and "$probfile" are not getting expanded, because otherwise there would be the contents of them in the error message.
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