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TroubleShooting & FAQs

Auden Cote-L'Heureux edited this page 2025-01-17 10:13:20 -05:00

Table of Contents

• Troubleshooting
• Overview
• FAQs
• Where can I find the figures and databases referred to here
• How do I set up my names and fasta files?
• What should I look for if I get no output from EukPhylo part 2?

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Troubleshooting

Overview

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 or tail 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

Where can I find the figures and databases referred to here

• Most items are found in our figshare folder

How do I set up my names and fasta files?

Required elements are:

• unique 10 digit code for each taxon (e.g. Op_me_Hsap for humans, Ba_pg_Ecol for E. coli)
• some unique identifier
• 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 EukPhylo part 2?

• Check your folder structure, input files, and the scripts.