Dear @genomax, Initially I used the test data and it works fine as I mentioned earlier. Then I have used my data including the assembled draft genome (.fna) of bacterial strains and their corresponding .ptt files as specified in the manual genome files (.fna) kept in GenomeSequence folder and annotation files (.ptt) kept in GenomeAnnotation folder. Both folder have been kept in input folder. I tried to run the executive file pgax and started my analysis by clicking Get Start button and then I have clicked Genome Alignment button, the process have been completed successfully. Further, I followed Orthologs analysis by clicking the same, and chosen Nucleotide Sequence Based with 70 % Identity and Coverage as well. But this time it ran without giving result. The resulting folder namely GenomeOrthologsCluster folder having 1kb sized OrthologsCluster file, which has the following strings only Cluster ID citri oryzae phas. Even I tried with the complete genome strains, but the result is same. I ran this in windows 10 OS.

Dear @RamRS, I checked my input data, which is same like test data. It differs in terms of size only, my each genome file has 5MB, whereas the test data is around 2.5 to 5 MB. I tried both complete and draft genome sequences as well, but both stops working in Orthologs analysis process. If it possible I can upload my dataset for your reference. Please let me know, how to upload my dataset here.