Question

I understand this is usually to do with recursion, except I am pretty sure I am not doing this.
On each time round the loop it gives a segmentation error pointing to the for loop’s line.

for file in $DATAFOLDER*; do
    echo $file;
    filename=$(basename $file);
    echo $filename;
    echo "$DESTFOLDER$SUBFOLDER${filename%%.*}"
    pwd
    # move data to cppapplication folder
    cp -R "$file" "$DESTFOLDER";
    sleep 1
    # create subdirectory
    mkdir "$SUBFOLDER";
    # create new folder for extracted data
    mkdir "$DESTFOLDER$SUBFOLDER${filename%%.*}";
    # copy MassLynx header file into new folder (get the description info)
    cp "$file/_HEADER.TXT" "$DESTFOLDER$SUBFOLDER${filename%%.*}";
    # run the cppapplication
    # <program> <project file> <MassSpectrum> <Mobilogram> <bins in Da> <extract m/z ranges>
    ./cppapplication.exe "$filename" 0 1 1 0 ;
    # fix last character comma bug
    sed -i '$ s/,$//g' MassMobility.txt
    # move the created files into the new folder
    mv Mobilogram.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";
    mv MassMobility.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}"; 
    mv MassMobilityXaxis.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";
    mv MassMobilityYaxis.txt "$DESTFOLDER$SUBFOLDER${filename%%.*}";    
    # get driftscope quicklook image
    sleep 3
    python "C:\Users\ganesh\Dropbox\PhD\03_Amphitrite\CppApplication\quicklook_driftscope.py" "$DESTFOLDERWINDOWS$SUBFOLDERWINDOWS" "${filename%%.*}" "$DESTFOLDERWINDOWS$SUBFOLDERWINDOWS${filename%%.*}";


    # remove MassLynx Project
    rm -r "$filename";

done

Aside from the copying of the file, I don’t think the loop has any contact with the original folder being looped through.

This is the error:

./extract_all_projects.sh: line 26:  7500 Segmentation fault      (core dumped) 

I have no idea what the problem is as “cppapplication.exe” works fine on these files if run outside of the bash script.

Answer 1

Your $filename could be empty or not as expected. I’m sure the segfault is the cppapplication.exe crashing (Why didn’t you tell us what line 26 is?) To test this, try

./cppapplication.exe "" 0 1 1 0

and see if it segfaults. If I had to guess: the app tries to open a file but doesn’t check the return value and soldiers on with a NULL pointer.

BTW, all except the first semicolon in your script are useless. The shell is not C 🙂