Output with no results and tdg09 getting stuck #3
Description
Hello,
We encountered a few issues with runs in tdg09. We are using it to detect convergent evolution across a range a vertebrate species and genes.
At first, we ran a limited dataset, tens of alignments with 19-25 sequences each belonging to a separate species. It mostly worked fine, however some output files did not produce results (only 1.2 kb, while others are usually a few hundred kb).
As a second step, we increased the dataset to a about 6000 gene alignments, with the same number of sequences per alignment as above. We tried running tdg09 in a bash script in a for loop, where a list of input data is used to make steps for the loop. Here is where more problems occurred. Usually after a few minutes it gets stuck on one input file and doesn't move to the next step. If rerun the file it gets stuck on, is not the same. We tried fixing this by removing the loop and creating a bash script with a separate line for every input file, however the problem persists. In addition, we still encounter output files with no results.
The issue of the programme getting stuck was solved using the timeout function when running tdg09 in a for loop. However, from about 6000 files approximately 1200 output files produced no results. When only those 1200 files were re-run, about 40 produced results, while the remaining still did not work.