Repeatmasker Crashes Before End Of Run With "Can'T Fork..."
I've been trying to run RepeatMasker but it keeps crashing with the error "Can't fork...". In the RepeatMasker script source code, this is here:
FORK: {
if ( $pid = fork ) {
$flag = 1;
waitpid( $pid, 0 ); #Waits for child to finish...
my ( $status ) = $?;
if ( WIFSTOPPED( $status ) ) {
my ( $signal ) = WSTOPSIG( $status );
print "\nforksys: Program terminated by a signal $signal.\n";
print "The executing command was: $cmd\n";
return 1;
}
if ( WIFEXITED( $status ) ) {
my ( $temp ) = WEXITSTATUS( $status );
return $temp;
}
if ( WIFSIGNALED( $status ) ) {
my ( $signal ) = WTERMSIG( $status );
print "\nforksys: Program terminated by a signal $signal.\n";
print "The executing command was: $cmd\n";
return 1;
}
}
elsif ( defined $pid ) {
exec( "$cmd" ) or die "Exec $cmd failed\n";
}
elsif ( $! =~ /No more process/o ) {
print "$!\n";
sleep 5;
redo FORK;
}
else {
die "Can't fork...\n";
}
}
}
any idea what parameter could be causing this or how it can be debugged? I ran RM with 6 processors and sensitive search but am now changing it to the "qq" option ("quick and dirty search") and giving it only 1 processor, to see if that helps in case it's a weird threading thing that happens. any thoughts on this?? thank you.
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Couldn't say why, but you're running into a problem when RepeatMasker tries to spawn a new process. That's an unusual problem to have, thus the perfunctory error message. Update your question after trying with a single execution thread.