error when running .awk script

Question

I have an awk script:

BEGIN { FS="_" }
/^>/ {
    id=$1;p=$2; wild=$3;subs=$4; c=$NF; next
}
{
    if (p-10<1) s=1
    else if (p+10>length($0)) s=length($0)-20
    else s=p-10
    print id"_"p"_"wild"_"subs">\n"substr($0,s,p-s) c substr($0,p+1,21-p+s)
}

and when I run I get the following:

$ cat test1.fasta | awk -f snp_flank.awk
bash: /usr/bin/awk: /usr/bin/awk: bad interpreter: Too many levels of symbolic links

what does this mean?

extra info:

$ ls -l /usr/bin/awk
lrwxrwxrwx 1 root root 21 2011-12-07 16:47 /usr/bin/awk -> /etc/alternatives/awk


$ head -n10 /usr/bin/awk
#!/usr/bin/awk -f

BEGIN { FS="_" }
/^>/ {
    id=$1;p=$2; wild=$3;subs=$4; c=$NF; next
}
{
    if (p-10<1) s=1
    else if (p+10>length($0)) s=length($0)-20
    else s=p-10

it appears I have accidentally replaced awk with an awk script! sorry! how do I fix this? would simply reinstalling awk sort this out?

What is /usr/bin/awk on that system? What do file /usr/bin/awk and head -n1 /usr/bin/awk say? — Etan Reisner
– Etan Reisner, Commented Mar 25, 2015 at 15:12
What is the result of the command: ls -l /usr/bin/awk ? Is this file a symbolic link to another file? I think there is a link loop. — Sylvain Bugat
– Sylvain Bugat, Commented Mar 25, 2015 at 15:13
it appears I have overwritten the awk program with my awk script!! how this happened i do not know. would a simple re-install of awk work? — brucezepplin
– brucezepplin, Commented Mar 25, 2015 at 15:24
Make sure you don't do software development as root. Make sure no-one except root can modify the directory /usr/bin (or /bin, /sbin, /usr/sbin, /etc, etc), and that no-one except root can modify the files in those directories. You should not be able to overwrite /usr/bin/awk running as an ordinary mortal user. — Jonathan Leffler
– Jonathan Leffler, Commented Mar 25, 2015 at 15:46

Camusensei · Accepted Answer · 2015-04-24 10:39:12Z

1

You have accidentally overwritten /usr/bin/awk.

Reinstall awk on your system.

sudo apt-get install --reinstall gawk

or

sudo yum reinstall gawk

depending on your system.

answered Apr 24, 2015 at 10:39

Camusensei

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