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issue with AGUSTUS

3

Hi, I have tried to resolve this issue but failed to do so while using UFCG. Please help asap. ERROR! AUGUSTUS-PPX config file is absent or improperly formatted. I get...

Keevai09

Could not initialize class envs.config.GenericConfig

5

I have intalled ufcg on WSL, however, when I used the same way (mamba install -y ufcg) to install it on ubuntu 22.04.2 LTS, it got wroing. `ufcg -u Exception...

jungleblack007

ITS genes not being found

5

Hello, Please, I have done the "ufcg download -t full" and when I run the profile analysis with --set NUC , the tool is not finding any ITS gene for...

rissidaniel

ERROR! Tree file of gene COX2 not found : trees2/aligned_COX2_pro.zZ.fasta.treefile

5

Greetings, I getting said error when running the tree command, it also seems the process does not complete because of this. I'm not able to determine what is causing the...

salvatierra8

Can you add a new gene in the list and run the whole analysis from profile to tree?

1

Hi, I was just wondering if there is a way to add an extra gene(s)on top of 61 marker genes, in the core gene list before we run the analysis?...

kusandeep

v1.0.2 augustus issue

6

When running ufcg (v1.0.2) profile, I get this error message: `ERROR! Failed subcommand :augustus --optCfgFile=/mnt/gpfs/seb/Applications/UFCG/config/ppx.cfg --predictionStart=24228 --predictionEnd=44228 --proteinprofile=/mnt/gpfs/seb/Applications/UFCG/config/model/pro/RPB2.hmm /home/sebr/seb/Database/Fungus_DB/UFCG/tmp/Lobtra1/tmp/Lobtra1/Lobtra1_scaffold_92.fna > /home/sebr/seb/Database/Fungus_DB/UFCG/tmp/Lobtra1/tmp/Lobtra1/Lobtra1_scaffold_92_p34228_RPB2.gff` I checked and this same genome dealt with normaly...

Sebastien-Raguideau

Error! metadata file improperly formatted

2

Hi - I installed ufcg using conda, and used the setup commands in the instructions. I am hit with this error when using the ufcg profile: `ufcg profile -i directory_with_sequences...

Ellouzlab

ERROR! java.io.IOException: Failed to list contents of /tmp/netdata-updater-hAcEdu4h9c

1

 Based [on the tutorial](https://ufcg.steineggerlab.com/ufcg/tutorial), I tried to command with my sample and got the above error, This is my command: ```bash ufcg profile --input WI0722303A01_sample/seq --output WI0722303A01_sample/out --set PRO...

Truongphi20

how to change busco databases?

4

For example, I want to use the agaricales_odb10 as reference database to pick single copy orthologs, how can I change the Fungi_odb10 to Agaricales_odb10?

jungleblack007

Java OutOfBoundsException on some genomes

1

Hello, I am using the latest version of the pipeline (v.1.0.3) and I am testing a large group of genomes from ncbi (very variable in quality) using the profile module...

BrigidaGallone