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Updated TroubleShooting & FAQs (markdown)

Godwin Ani 2024-08-14 13:35:36 -04:00
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TroubleShooting-&-FAQs.md

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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
## 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)