From 944f2afc8e3e6e9c9c47ce576214bac281bb7c88 Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Fri, 17 Jan 2025 10:13:20 -0500
Subject: [PATCH] Updated TroubleShooting & FAQs (markdown)

---
 TroubleShooting-&-FAQs.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/TroubleShooting-&-FAQs.md b/TroubleShooting-&-FAQs.md
index 564c9c4..a77b561 100644
--- a/TroubleShooting-&-FAQs.md
+++ b/TroubleShooting-&-FAQs.md
@@ -1,14 +1,14 @@
 
-# [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)
 
@@ -19,6 +19,6 @@ Required elements are:
  * 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.