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Updated TroubleShooting & FAQs (markdown)

Auden Cote-L'Heureux 2025-01-17 10:13:20 -05:00
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TroubleShooting-&-FAQs.md

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# [Troubleshooting](https://github.com/Katzlab/PhyloToL-6/wiki/TroubleShooting-&-FAQs#Troubleshooting)
# [Troubleshooting](https://github.com/Katzlab/EukPhylo/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.
EukPhylo 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.
* Check ALL error/log files : Use commands like head <log-file> or tail <log-file> to quickly look at the EukPhylo 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.
# [FAQs](https://github.com/Katzlab/PhyloToL-6/wiki/TroubleShooting-&-FAQs#FAQs)
# [FAQs](https://github.com/Katzlab/EukPhylo/wiki/TroubleShooting-&-FAQs#FAQs)
## Where can I find the figures and databases referred to here
* Most items are found in our [figshare folder](https://figshare.com/account/home#/projects/196552)
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* for Part 2, each sequence name should end with a 10 digit code for each gene family (e.g. OG6_123456)
* example: >Op_me_Hsap_HP067328_OG6_124578
## What should I look for if I get no output from PTL6p2?
## What should I look for if I get no output from EukPhylo part 2?
* Check your folder structure, input files, and the scripts.