Hi,
Any attempt to work with the Silva seed on v1.36 (Win64) causes immediate crash, e.g.:
mothur >
align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.seed_v123.align)
[ERROR]: has occurred in the MothurOut class function mothurConvert. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
Changing the file name or extension doesn’t help. Changing to Mothur v1.35 solves the problem 
P.
Thanks for reporting this bug. When we added the option to seed random in version 1.36, we did not account for “seed” being part of a filename. We have fixed this issue and the change will be part of the next release. As a workaround you can change the name of the reference to not include the word seed.
mothur > align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.seed_v123.align)
could be:
mothur > align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v123.align)
I looked into the code, and find where the problem is.
File: commandfactory.cpp
Here is my fix:
int CommandFactory::checkForRedirects(string optionString) {
cerr << “CommandFactory::checkForRedirects(”
<< optionString << “)\n”
<< " Kemin has implemented this function!\n";
// trying to parse out outputdir=string, inputdir=blabla, seed=123
// and ignoring all others
string::size_type i=0, ii=0, j; // don’t use unsigned int, cause infinite loop
map<string, string> kvpair;
ii = optionString.find(’,’, i);
string kv;
while (ii != string::npos) {
kv = optionString.substr(i, ii-i);
kvpair.insert(extractPair(kv));
i=ii+1;
while (i != string::npos && isspace(optionString_))
++i;
if (i == string::npos) {
cerr << “while looking for ‘,’ inside " << optionString
<< " reached the end of string!\n”;
break;
}
ii = optionString.find(’,’, i);
}
// last option
kv = optionString.substr(i);
kvpair.insert(extractPair(kv));
// process the options
map<string,string>::const_iterator mit;
for (mit = kvpair.begin(); mit != kvpair.end(); ++mit) {
if (mit->first == “outputdir”) {
//user has set outputdir in command option string
string outputOption = mit->second;
if(m->mkDir(outputOption)) {
setOutputDirectory(outputOption);
m->mothurOut("Setting output directory to: " + outputOption);
m->mothurOutEndLine();
}
else {
cerr << "failed to mkdir: " << outputOption << endl;
}
}
else if (mit->first == “inputdir”) {
//user has set inputdir in command option string
string inputOption = mit->second;
if(m->dirCheck(inputOption)) {
setInputDirectory(inputOption);
m->mothurOut(“Setting input directory to: " + inputOption);
m->mothurOutEndLine();
}
else {
cerr << “Failed to find input directory: " << inputOption << endl;
}
}
else if (mit->first == “seed”) {
// intended to parse the seed=123 option
string intputOption = mit->second;
bool seed = false;
int random;
if (intputOption == “clear”) {
random = time(NULL);
seed = true;
}
else {
if (m->isInteger(intputOption)) {
m->mothurConvert(intputOption, random);
seed=true;
}
else {
m->mothurOut(”[ERROR]: Seed must be an integer.”);
m->mothurOutEndLine(); seed = false;
}
}
if (seed) {
srand(random);
m->mothurOut("Setting random seed to " + toString(random) + “.\n\n”);
}
}
}
return 0;
…
The incorrect part of the original fraction:
pos = optionString.find(“seed”);
if (pos != string::npos) { //user has set inputdir in command option string
string intputOption;
bool foundEquals = false;
for(int i=pos; i<optionString.length(); i++){
if(optionString == ‘,’) break;
else if(optionString == ‘=’) {
foundEquals = true;
}
if (foundEquals) {
intputOption += optionString;
}
}
if (intputOption[0] == ‘=’) {
intputOption = intputOption.substr(1);
}
bool seed = false;
int random;
if (intputOption == “clear”) {
random = time(NULL);
seed = true;
}
else {
if (m->isInteger(intputOption)) {
m->mothurConvert(intputOption, random); seed=true;
}
else {
m->mothurOut("[ERROR]: Seed must be an integer.");
m->mothurOutEndLine(); seed = false;
}
}
if (seed) {
srand(random);
m->mothurOut("Setting random seed to " + toString(random) + “.\n\n”);
}
}___