Hi , 
I have a report which have 48000  records  , when i run a report using synchronous Approach in apex code , it will only return 2000 records  so in order to overcome this problem i have used filter in report but after returning 4000 records it throw exception " FATAL_ERROR System.LimitException: reports:Too many query rows: 50001 "  . (I can't Use Asynch Approach as i am using this class inside batch class).
In order to Apply Filter i am using Autonumber field and sort them in ascending order, Please have a look to my code and help me to figure out the problem , Thanks to All In Advance.


String reportId='00Of1000004jG5h'; // Report Id
Integer filterNumber=0; // Set Lower Row Limit For Filter 
boolean getAllData=False;
integer count=0;

while(getAllData==false) {
Reports.ReportDescribeResult describe = Reports.ReportManager.describeReport(reportId); // describe report metadata
            Reports.ReportMetadata reportMd = describe.getReportMetadata();
    
                string b =reportMd.getDetailColumns()[0]; //get Filtered Column From Report , it is Autonumber Field
                String column1=b;
                Integer value1=filterNumber;
                String operator1='greaterOrEqual';
    
              Reports.ReportFilter filter = reportMd.getReportFilters()[0];// get Filter and Update filter values in apex
             
            filter.setColumn(column1);
            filter.setValue(string.valueOf(value1));
            filter.setOperator(operator1);
             Integer value2=value1+2000; // Upper Limit for Second Filter
            String operator2='lessOrEqual';
                
             Reports.ReportFilter filter1 =reportMd.getReportFilters()[0]; // Second Filter to report on same column 
            filter1.setColumn(column1);
            filter1.setValue(string.valueOf(value2));
            filter1.setOperator(operator2);
    
        
           // Run a report synchronously
            Reports.reportResults ActiveISOContacts = Reports.ReportManager.runReport(reportId,reportMd, true);
            getAllData=ActiveISOContacts.getAllData();
           system.debug(ActiveISOContacts.getAllData());//this will return true and false .

           // Get the fact map from the report results
            Reports.ReportFactWithDetails factDetails = (Reports.ReportFactWithDetails)ActiveISOContacts.getFactMap().get('T!T');
            //create a list of report rows and populate it with the result rows from fact map
            List<Reports.ReportDetailRow> reportRows = factDetails.getRows();
            filterNumber =filterNumber+reportRows.size();
            count++;
                system.debug(filterNumber);
    system.debug(count);
    }