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Hi,

Am doing the tutorial with my own dataset (Staphylococci) and it is great. However, at the "Evaluate genome quality" step I struggled with two things:

1. it is unclear how the removedGenomes_25.txt is created; I created it manually, but there is no clear instruction on how to generate it. A comment may be helpful.
2. the command line "chewBBACA.py ExtractCgMLST -i cgMLST_all.tsv -o cgMLST_25 -g removedGenomes_25.txt" is incorrect, the "-g" should be "--g" (double hyphen)

Just the icing on the cake! :)

The file required in one of the first steps in the tutorial is missing: Streptococcus_agalactiae.trn

Could you please supply it as part of the tutorial

In the tutorial, "Now the file cgMLST_completegenomes/cgMLST.tsv can be concatenated with the allele call result from the 680 genomes results_all/results_20180202T112710/results_alleles.tsv", I don't know how to concatenate these two files to get the cgMLST_all.tsv

Hi @rfm-targa and authors,

Thank you very much for writing an amazing tool.

I have an external schema for stenotrophomonas through which I want to do cgMLST analysis and then generate a core gene alignment. May I know if the alignment could be created using cgMLST_completegenomes/Presence_Absence.tsv? May I know, if there is there any easy way to do with chewBBACA? Can request your advice. Thanks very much in advance!

Edit1: Hi. With a bit of reading, I think what I need is: To generate core gene alignment using cgMLST_completegenomes/cgMLST.tsv. Can I kindly request advice if my approach is correct and help in generating alignment so that I do not need to reinvent the wheel.

Heisann guys.

I am doing running the chewbacca in a conda environment (tried to downloaded chewbbaca both by conda and pip), and have basically copy pasted all your commands etc. I encounter error msg when running allelcall:

^MProcessing GCA-000007265-protein10.fasta. Start 22:19:33-22/07/2019 Locus 2 of 3130. Done 0%.some error occu$
%i format: a number is required, not NoneType
Error on line 466

It is numerous times for most loci and results in non-valid error allele assignments. I went into the schema_seed and had a look at the different loci too, they just look normal.
what am I doing wrong?

AK

Hi,

Can request to know how to solve this error? Many thanks in advance.

chewBBACA.py AlleleCall -i .genomes/ -g listgenes_core.txt -o results --cpu 6 --ptf Streptococcus_agalactiae.trn

chewBBACA version: 2.5.5
Authors: Mickael Silva, Pedro Cerqueira, Rafael Mamede
Github: https://github.com/B-UMMI/chewBBACA
Wiki: https://github.com/B-UMMI/chewBBACA/wiki
Tutorial: https://github.com/B-UMMI/chewBBACA_tutorial
Contacts: [email protected]

==========================
  chewBBACA - AlleleCall
==========================
It seems that your schema was created with chewBBACA 2.1.0 or lower.
It is highly recommended that you run the PrepExternalSchema process to guarantee full compatibility with the new chewBBACA version.
If you wish to continue, the AlleleCall process will convert the schema to v2.5.5, but will not determine if schema structure respects configuration values.
Do you wish to proceed?
yes

Adding Prodigal training file to schema...
Created listgenes_core.txt/Streptococcus_agalactiae.trn

Creating file with schema configs...
Traceback (most recent call last):
  File "/storage/apps/anaconda3/bin/chewBBACA.py", line 10, in <module>
    sys.exit(main())
  File "/storage/apps/anaconda3/lib/python3.6/site-packages/CHEWBBACA/chewBBACA.py", line 1549, in main
    functions_info[process][1]()
  File "/storage/apps/anaconda3/lib/python3.6/site-packages/CHEWBBACA/chewBBACA.py", line 414, in allele_call
    schema_directory)
  File "/storage/apps/anaconda3/lib/python3.6/site-packages/CHEWBBACA/utils/auxiliary_functions.py", line 224, in write_schema_config
    pickle_dumper(config_file, params)
  File "/storage/apps/anaconda3/lib/python3.6/site-packages/CHEWBBACA/utils/auxiliary_functions.py", line 77, in pickle_dumper
    with open(pickle_out, 'wb') as po:
NotADirectoryError: [Errno 20] Not a directory: 'listgenes_core.txt/.schema_config'

Is there a way to create a file analysis/listgenes_core.txt? I don't see any instructions mentioning it.

Hi, I am new to chewBBACA. Through my practice and I noticed in the process of CreateSchema we should input a file suffixed with .trn, and I also was not familiar with prodigal. The codes are blow:

chewBBACA.py CreateSchema -i complete_genomes/ --cpu 6 -o schema_seed --ptf Streptococcus_agalactiae.trn

So, could you mind to tell me how to use prodigal to make a training set? Thanks.

I tried to creat salmonella scheme by myself and entered the command line as follows"chewBBACA.py CreateSchema -i cgMLST/ -o Salmonellascheme --cpu 8 --ptf training/Salmonella_enterica.trn", but it prompted error message "chewbbaca scheme creation error:BLAST Database error: No alias or index file found for protein database [/home/qifeng/temp/protogenome1/blastdbs/protogenome1_proteins_db] in search path [/home/qifeng::" halfway. How can I fix it.