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 #!/usr/bin/perl5.8.8

use strict;
...
chomp $infile;
open (my $INFILE,"<", $infile)
close ($INFILE);

 #PBS -t 1-10
#PBS -l walltime=48:00:00
/usr/bin/perl /chongle/jeri/timecheck/MUSCLEHMM.pl $PBS_ARRAYID > /cho
+ngle/jeri/timecheck/output.$PBS_ARRAYID.txt 2> /chongle/jeri/timechec
+k/error.$PBS_ARRAYID.txt

#Use of uninitialized value in concatenation (.) or string at line 18.
#Use of uninitialized value in scalar chomp at /chongle/jeri/timecheck
+/MUSCLEHMM.pl line 19.
#Use of uninitialized value in open at /chongle#/jeri/timecheck/MUSCLE
+HMM.pl line 20.
#No such file or directory at /chongle/jeri/timecheck/MUSCLEHMM.pl lin
+e 20.