merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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anvi-gen-genomes-storage complains about bad characters #2122

Closed 17863952296 closed 11 months ago

17863952296 commented 11 months ago

when I run the command

anvi-gen-genomes-storage -e external-genomes.txt -o Streptomyces-GENOMES.db

it happened:

Config Error: Well, the genome name "CRD01C3C1.db" contains characters that anvi'o does not
like :/ Please limit the characters to ASCII letters, digits, and the underscore ('_') character.

but when I check the CRD01C3C1.db (anvi-db-info CRD01C3C1.db), it is :

DB Info (no touch)
===============================================
Database Path ................................: CRD01C3C1.db
description ..................................: [Not found, but it's OK]
db_type ......................................: contigs (variant: unknown)
version ......................................: 20

DB Info (no touch also)
===============================================
project_name .................................: CRD01C3C1.db
contigs_db_hash ..............................: hash8cba85b4
split_length .................................: 20000
kmer_size ....................................: 4
num_contigs ..................................: 92
total_length .................................: 8030552
num_splits ...................................: 406
gene_level_taxonomy_source ...................: None
genes_are_called .............................: 1
external_gene_calls ..........................: 0
external_gene_amino_acid_seqs ................: 0
skip_predict_frame ...........................: 0
splits_consider_gene_calls ...................: 1
creation_date ................................: 1695088071.83526
trna_taxonomy_was_run ........................: 1
trna_taxonomy_database_version ...............: v89
scg_taxonomy_was_run .........................: 1
scg_taxonomy_database_version ................: v202.0
gene_function_sources ........................: Pfam,KEGG_Module,KEGG_Class,Transfer_RNAs,COG20_FUNCTION,COG20_PATHWAY,COG20_CATEGORY,KOfam
modules_db_hash ..............................: 45b7cc2e4fdc
Database_Path ................................: CRD01C3C1.db

* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be
extremely careful.

AVAILABLE GENE CALLERS
===============================================
* 'prodigal' (7,062 gene calls)
* 'Transfer_RNAs' (72 gene calls)
* 'Ribosomal_RNA_23S' (1 gene calls)
* 'Ribosomal_RNA_16S' (1 gene calls)

AVAILABLE FUNCTIONAL ANNOTATION SOURCES
===============================================
* COG20_CATEGORY (5,492 annotations)
* COG20_FUNCTION (5,492 annotations)
* COG20_PATHWAY (1,280 annotations)
* KEGG_Class (757 annotations)
* KEGG_Module (757 annotations)
* KOfam (3,697 annotations)
* Pfam (11,648 annotations)
* Transfer_RNAs (72 annotations)

AVAILABLE HMM SOURCES
===============================================
* 'Archaea_76' (76 models with 34 hits)
* 'Bacteria_71' (71 models with 74 hits)
* 'Protista_83' (83 models with 8 hits)
* 'Ribosomal_RNA_12S' (1 model with 0 hits)
* 'Ribosomal_RNA_16S' (3 models with 1 hit)
* 'Ribosomal_RNA_18S' (1 model with 0 hits)
* 'Ribosomal_RNA_23S' (2 models with 1 hit)
* 'Ribosomal_RNA_28S' (1 model with 0 hits)
* 'Ribosomal_RNA_5S' (5 models with 0 hits)
* 'Transfer_RNAs' (61 models with 72 hits)

so , I didn't find "/" character. why it errored?

meren commented 11 months ago

it is about how you named your genomes in the external-genomes.txt.

please check the first column of names in that file.