From aafa36f3b9aa2dc8b405ce3e4d44f238035518ea Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Wed, 14 Aug 2024 13:49:29 -0400 Subject: [PATCH] Updated TroubleShooting & FAQs (markdown) --- TroubleShooting-&-FAQs.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/TroubleShooting-&-FAQs.md b/TroubleShooting-&-FAQs.md index 71c0064..564c9c4 100644 --- a/TroubleShooting-&-FAQs.md +++ b/TroubleShooting-&-FAQs.md @@ -2,8 +2,9 @@ # [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 or tail 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 or tail 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. @@ -19,5 +20,5 @@ Required elements are: * 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.