[GlimmerHMMJ] error message

[syintel87]

Hello,
When I ran "trainGlimmerHMM", my job was exited.
Would you please give me a piece of advice if you have any idea about the error message?
The error message says:

Training data created successfully! Check exons.dat and seqs for accuracy.
ERROR 43: /home/scha/4_gene_prediction/GlimmerHMM/train/build1 exited funny: -1

Thank you in advance.

[syintel87]

ERROR MESSAGE:

Training data created successfully! Check exons.dat and seqs for accuracy.
ERROR 43: /home/scha/4_gene_prediction/GlimmerHMM/train/build1 exited funny: -1 at trainGlimmerHMM line 338.

CODE: line 338 is underlined and in red.

# change working directory to $traindir
chdir "$traindir" or die printerr("ERROR 29: Can't cd to $traindir: $!\n");
print L "Training data created successfully! Check exons.dat and seqs for accuracy.\n\n";

%seqs=();

my ($istacc,$istdon,@list);

############ train splice sites
############
{

# form the training files for the splice sites of length 80 bp
formacc("exons.dat","seqs","train.acc.80");
die printerr("ERROR 30: creating acceptor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.acc.80";
formfacc("exons.dat","seqs","train.facc.80");
die printerr("ERROR 31: creating false acceptor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.facc.80";
formdon("exons.dat","seqs","train.don.80");
die printerr("ERROR 32: creating donor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.don.80";
formfdon("exons.dat","seqs","train.fdon.80");
die printerr("ERROR 33: creating false donor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.fdon.80";
clean("train.acc.80","acc","train.acc.clean");
die printerr("ERROR 34: no acceptors for training.\n") unless -s "train.acc.clean";
clean("train.facc.80","acc","train.facc.clean");
die printerr("ERROR 35: no false acceptors for training.\n") unless -s "train.facc.clean";
clean("train.don.80","don","train.don.clean");
die printerr("ERROR 36: no donors for training.\n") unless -s "train.don.clean";
clean("train.fdon.80","don","train.fdon.clean");
die printerr("ERROR 37: no false donors for training.\n") unless -s "train.fdon.clean";

my $status=system("mv train.acc.clean train.acc.80");
die printerr("ERROR 38: mv exited funny: $?") unless $status ==0;
$status=system("mv train.facc.clean train.facc.80");
die printerr("ERROR 40: mv exited funny: $?") unless $status ==0;
$status=system("mv train.don.clean train.don.80");
die printerr("ERROR 41: mv exited funny: $?") unless $status ==0;
$status=system("mv train.fdon.clean train.fdon.80");
die printerr("ERROR 42: mv exited funny: $?") unless $status ==0;

# form the markov files for the splice sites
my $command="$scriptdir/build1";
$command="$scriptdir/build2" if($build!=1);
$status=system("$command train.acc.80 acc1.mar +44,72");
die printerr("ERROR 43: $command exited funny: $?") unless $status ==0;
$status=system("$command train.facc.80 acc1.mar +44,72 -append");
die printerr("ERROR 44: $command exited funny: $?") unless $status ==0;
$status=system("$command train.don.80 don1.mar +5,20");
die printerr("ERROR 45: $command exited funny: $?") unless $status ==0;
$status=system("$command train.fdon.80 don1.mar +5,20 -append");
die printerr("ERROR 46: $command exited funny: $?") unless $status ==0;


# form the MDD trees
$status=system("$scriptdir/karlin train.acc.80 outex 44 72 24");
die printerr("ERROR 47: $scriptdir/karlin exited funny: $?") unless $status ==0;
$status=system("$scriptdir/karlin train.don.80 outin 5 20 5");
die printerr("ERROR 48: $scriptdir/karlin exited funny: $?") unless $status ==0;

@list=();
$istacc=MDD("outex","acc",44);
@list=();
$istdon=MDD("outin","don",5);

# cleaning the train.*, outex?*, outin?*, outf* files
system("rm train.* outex?* outin?* outf*");

# form the train files for the splice sites of length 162
formacc162("exons.dat","seqs","train.acc");
die printerr("ERROR 49: creating acceptor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.acc";
formfacc162("exons.dat","seqs","train.facc");
die printerr("ERROR 50: creating false acceptor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.facc";
formdon162("exons.dat","seqs","train.don");
die printerr("ERROR 51: creating donor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.don";
formfdon162("exons.dat","seqs","train.fdon");
die printerr("ERROR 52: creating false donor sites. Not enough data or check input files for wrong format.\n")
unless -s "train.fdon";
clean162("train.acc","acc","train.acc.clean");
die printerr("ERROR 53: no acceptors for training.\n") unless -s "train.acc.clean";
clean162("train.facc","acc","train.facc.clean");
die printerr("ERROR 54: no false acceptors for training.\n") unless -s "train.facc.clean";
clean162("train.don","don","train.don.clean");
die printerr("ERROR 55: no donors for training.\n") unless -s "train.don.clean";
clean162("train.fdon","don","train.fdon.clean");
die printerr("ERROR 56: no false donors for training.\n") unless -s "train.fdon.clean";


$status=system("mv train.acc.clean train.acc");
die printerr("ERROR 57: mv exited funny: $?") unless $status ==0;
$status=system("mv train.facc.clean train.facc");
die printerr("ERROR 58: mv exited funny: $?") unless $status ==0;
$status=system("mv train.don.clean train.don");
die printerr("ERROR 59: mv exited funny: $?") unless $status ==0;
$status=system("mv train.fdon.clean train.fdon");
die printerr("ERROR 60: mv exited funny: $?") unless $status ==0;


my $nacc=`cat train.acc|wc -l`; chomp($nacc);
my $ndon=`cat train.don|wc -l`; chomp($ndon);
my $nfacc=`cat train.facc|wc -l`; chomp($nfacc);
my $nfdon=`cat train.fdon|wc -l`; chomp($nfdon);

print L "\nAcceptor sites for training: $nacc\n";
print L "False acceptor sites for training: $nfacc\n";
print L "Donor sites for training: $ndon\n";
print L "False donor sites for training: $nfdon\n";
if($nacc<100) {
print L "Increase the number of acceptor sites for a more accurate training!\n";
}
if($ndon<100) {
print L "Increase the number of donor sites for a more accurate training!\n";
}
print L "\n";


# form the training files for coding/noncoding portions
formcodncod("train.acc","acc.in","acc.ex");
formcodncod("train.facc","facc.in","facc.ex");
formcodncod("train.don","don.ex","don.in");
formcodncod("train.fdon","fdon.ex","fdon.in");


# form the cod/non-cod scoring files
$status=system("$command acc.ex score_ex.acc");
die printerr("ERROR 61: $command exited funny: $?") unless $status ==0;
$status=system("$command facc.ex score_ex.acc -append");
die printerr("ERROR 62: $command exited funny: $?") unless $status ==0;
$status=system("$command don.ex score_ex.don");
die printerr("ERROR 63: $command exited funny: $?") unless $status ==0;
$status=system("$command fdon.ex score_ex.don -append");
die printerr("ERROR 64: $command exited funny: $?") unless $status ==0;
$status=system("$command acc.in score_in.acc");
die printerr("ERROR 65: $command exited funny: $?") unless $status ==0;
$status=system("$command facc.in score_in.acc -append");
die printerr("ERROR 66: $command exited funny: $?") unless $status ==0;
$status=system("$command don.in score_in.don");
die printerr("ERROR 67: $command exited funny: $?") unless $status ==0;
$status=system("$command fdon.in score_in.don -append");
die printerr("ERROR 68: $command exited funny: $?") unless $status ==0;

# cleaning the *.ex, *.in files
system("rm *.ex *.in");


# score the results
my $command="$scriptdir/score";
$command="$scriptdir/score2" if($build!=1);
$status=system("$command train.acc train.facc train.don train.fdon score.acc score.don $istacc $istdon 1 > res.temp");
die printerr("ERROR 69: $command exited funny: $?") unless $status ==0;
$status=system("$scriptdir/falsecomp score.acc score.don false.acc false.don $nacc $nfacc $ndon $nfdon");
die printerr("ERROR 70: $scriptdir/falsecomp exited funny: $?") unless $status ==0;
# clean score.acc score.don
system("rm score.acc score.don res.temp");

# compute the $thracc and $thrdon values
$thracc=choose_thr("false.acc");
$thrdon=choose_thr("false.don");

print L "Default threshold value for the acceptor sites: $thracc\n";
print L "Default threshold value for the donor sites: $thrdon\n";

system("rm train.acc train.facc train.don train.fdon");
}