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 # [Troubleshooting](https://github.com/Katzlab/PhyloToL-6/wiki/TroubleShooting-&-FAQs#Troubleshooting)
+## Overview 
+PhyloToL is not a commercial package, and so it is on each researcher to investigate errors.  Here are a few starting points.
+* Be sure to have a ‘positive control’ for all files
+* Check ALL error/log files
+** Use commands like head <log-file> or tail <log-file> to quickly look at the PTL log files generated each time you submit a slurm job using sbatch
+** Errors might originate at the beginning (head) that affect results downstream
+** Usually the errors seen at the end of the run (tail) do no reflect where issues started; consult the Intermediate sub-folder in Output and/or other Katz lab members to track down the start of the issue
+* Common errors: Incorrect file paths, incorrect file names, dependencies version in slurm/shell scripts
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 ## Common errors in setting up PhyloToL include:
 * failure to name files or paths correctly (capitalization and spacing matter)
 * failure to control names of sequences (search for 10 digit code throughout wiki)