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Updated TroubleShooting & FAQs (markdown)

Godwin Ani 2024-08-14 13:49:29 -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 for each run. Also check the Intermediate sub-folder in Output to track down the issue
* 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 for each run. Also check the Intermediate sub-folder in Output to track down the issue.
* Be sure to delete the output folder of the previous run.
* Common errors: Incorrect file paths or names (capitalization and spacing matter), incorrect sequence names (search for 10 digit code throughout wiki), wrong dependencies version in slurm/shell scripts.
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* example: >Op_me_Hsap_HP067328_OG6_124578
## What should I look for if I get no output from PTL6p2?
* Check your folder structure, input files, and the scripts. Also make sure to delete the output folder from the previous run.
* Check your folder structure, input files, and the scripts.