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B-UMMI / chewBBACA

BSR-Based Allele Calling Algorithm
GNU General Public License v3.0
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No usable gene files in listGenes2Call.txt #20

Closed MNNatUA closed 5 years ago

MNNatUA commented 5 years ago

Hello, I'm a newbie and I’m encountering an error with ChewBBACA while doing allele calling.

Following are the command lines I used:

########Create Schema chewBBACA.py CreateSchema -i /home/Consensus/ --cpu 4 -o /home/Chewbbaca-Results --ptf /home/chewBBACA/CHEWBBACA/prodigal_training_files/Escherichia_coli.trn

---> Outputs include: folder /home/temp/, with 374 sub-folders of protogenomes and ORF.txt files for all the genomes; listGenes2Call.txt (0 bytes) and listGenomes2Call.txt (26.7kb) in /home/ChewBBACA/CHEWBBACA/

####### Allele Call chewBBACA.py AlleleCall -i /home/Consensus/ -g /home/temp/ --cpu 4 -o /home/Saturn-Chewbbaca-Results --ptf /home/chewBBACA/CHEWBBACA/prodigal_training_files/Escherichia_coli.trn

chewBBACA version 2.0.16 by Mickael Silva at https://github.com/B-UMMI/chewBBACA email contact: mickaelsilva@medicina.ulisboa.pt

'utf-8' codec can't decode byte 0x80 in position 0: invalid start byte ... 'utf-8' codec can't decode byte 0x80 in position 0: invalid start byte will use this training file : /home/chewBBACA/CHEWBBACA/prodigal_training_files/Escherichia_coli.trn blastp Will use this number of cpus: 4 Checking all programs are installed Checking Blast installed... True Checking Prodigal installed... True blast version is up to date, the program will continue

Starting Script at : 11:10:01-09/01/2019 checking if genome files exist.. checking if gene files exist.. ERROR! No usable gene files in listGenes2Call.txt

This file listGenes2Call.txt is indeed 0 byte in size. But I dont know why this happened.

Any help is appreciated.

jacarrico commented 5 years ago

Hi. Thanks for the contact! What is the contents of /home/Consensus/?

MNNatUA commented 5 years ago

Dear,

I have contacted Mickael Santos da Silvaand and have received suggestions to fix the problem. Many thanks for following up the post.

Best regards,

TheBready commented 5 years ago

Hi, I have the same issue. What was the solution to your problem? Best regards

jacarrico commented 5 years ago

@mickaelsilva or @MNNatUA Could you help @TheBready please?

mickaelsilva commented 5 years ago

The first step of creating the schema didn't work as expected. The output from should be a single folder, in your case "Chewbbaca-Results" (also advised to use "_" instead of "-" in file names . Maybe there was a problem with the files inside your "Consensus" folder. Be sure that inside that folder there is only fasta files of genomes.

You can first try to create a schema with a complete genome or a single genome file of your preference, then if it works try a new schema creation with your files.

This was the reply to the original poster, let me know if it helped @TheBready