This project forked from arnaudbelcour/gff_to_gbk
Convert GFF, fastas, annotation table and species name into Genbank.
License: GNU Lesser General Public License v3.0
This project is licensed under the GNU GPL-3.0-or-later, see the LICENSE file for details.
On directory mode, when we give a file with taxonomy values, having the full taxonomy and not the specie, the program only get the first value.
I'm going to create a branch and propose a modification
Example :
Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia marmotae
The taxon find is for "Bacteria".
If we reverse it, it will find the taxon for "Escherichia marmotae"
If the first element is not found (because does not exist) it will not try to find the parent.
Hello,
I did a annotation with eggnog-mapper on my new Pacbio assembly. The annotation and the output files are (look) OK. What I want to do is convert my GFF annotation file into a GenBank file. That's why I use emapper2gbk.
I have a single chromosome assembly >CP019962.1_RagTag , (I only show the beginning of the files) my gene predictions from proidgal :
>CP019962.1_RagTag_1 2 115 -1 ID=1_1;partial=10;start_type=ATG;rbs_motif=GGAGG;rbs_spacer=5-10bp;gc_cont=0.465
MTKEQKAVLKRALDHYGIDNQLTKAAEEMAELTKEICK
>CP019962.1_RagTag_2 358 468 -1 ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.342
MSWTMIFKKFEFPVLKVPVGNKVYIWLKKNINLLRV*
>CP019962.1_RagTag_3 446 2329 -1 ID=1_3;partial=00;start_type=GTG;rbs_motif=GGxGG;rbs_spacer=5-10bp;gc_cont=0.503
MQIEKLTKETILEDTTFEEIIDEKDEIYRQRLINDLTDRAAELGVKTKFTSLLKAYQKEE
KKMLQEQKKQLQEQNRARILQNLDRRTEFGSECYPDLRCGNWFADETGIRTFGMFGEVQA
my annotation.tsv file :
CP019962.1_RagTag_3 903814.ELI_1277 0.0 1239.2 COG5519@1|root,COG5519@2|Bacteria,1TRMV@1239|Firmicutes,24BJ9@186801|Clostridia 186801|ClostridiaL Psort location Cytoplasmic, score - - - - - - - - - - - - DUF927
CP019962.1_RagTag_4 903814.ELI_1276 3.4e-100 370.9 COG0358@1|root,COG0358@2|Bacteria 2|Bacteria L DNA primase activity -- 3.6.4.12 ko:K02316,ko:K17680 ko03030,map03030 - - - ko00000,ko00001,ko01000,ko03029,ko03032 - - -DUF3991,DnaB_C,Toprim_2,Toprim_3,Toprim_N,zf-CHC2
and my gff file :
CP019962.1_RagTag eggNOG-mapper CDS 1 35 69.7 + . ID=CP019962.1_RagTag_1740;em_target=903814.ELI_3509;em_score=69.7;em_evalue=3.2e-10;em_tcov=15.6;em_searcher=diamond;em_OGs=COG1668@1|root,COG1668@2|Bacteria,1V2WV@1239|Firmicutes,24IFP@186801|Clostridia;em_COG_cat=CP;em_desc=transmembrane transport;em_max_annot_lvl=186801|Clostridia;em_Preferred_name=;em_KEGG_ko=ko:K16906;em_KEGG_Pathway=ko02010,map02010;em_KEGG_Module=M00224;em_BRITE=ko00000,ko00001,ko00002,ko02000;em_KEGG_TC=3.A.1;em_PFAMs=
CP019962.1_RagTag eggNOG-mapper CDS 1 37 80.9 + . ID=CP019962.1_RagTag_1273;em_target=903814.ELI_4010;em_score=80.9;em_evalue=1.4e-13;em_tcov=100.0;em_searcher=diamond;em_OGs=COG0257@1|root,COG0257@2|Bacteria,1VK4F@1239|Firmicutes,24UGF@186801|Clostridia,25XP9@186806|Eubacteriaceae;em_COG_cat=J;em_desc=Belongs to the bacterial ribosomal protein bL36 family;em_max_annot_lvl=186801|Clostridia;em_PFAMs=Ribosomal_L36;em_Preferred_name=rpmJ;em_KEGG_ko=ko:K02919;em_KEGG_Pathway=ko03010,map03010;em_KEGG_Module=M00178;em_BRITE=br01610,ko00000,ko00001,ko00002,ko03011;em_GOs=
I get a GenBank file but without the CDS annotations :
LOCUS CP019962.1_RagTag 4424507 bp DNA BCT 05-NOV-2021
DEFINITION Firmicutes genome.
ACCESSION CP019962.1_RagTag
VERSION CP019962.1_RagTag
KEYWORDS Firmicutes.
SOURCE .
ORGANISM Firmicutes
Bacteria.
FEATURES Location/Qualifiers
source 1..4424507
/scaffold="CP019962.1_RagTag"
/db_xref="taxon:1239"
ORIGIN
1 gcttgcagat ctcttttgtc aattcagcca tctcttccgc ggccttggtg agctggttgt
61 caatgccgta atggtcaagt gcccttttta ggaccgcttt ctgttctttg gtcatttcat
121 cctcccgtag gtctcataaa tttcttgcaa cttatagttt tattttttaa ttgttataaa
I ran :
emapper2gbk genomes --fastanucleic EggMapper_Annot_Microbial_Assembly_v2_RagTag_Scaffolded.emapper.fna --fastaprot EggMapper_Annot_Microbial_Assembly_v2_RagTag_Scaffolded.emapper.genepred.faa --out test.gbk --gff EggMapper_Annot_Microbial_Assembly_v2_RagTag_Scaffolded.emapper.gff --annotation EggMapper_Annot_Microbial_Assembly_v2_RagTag_Scaffolded.emapper.annotation.tsv -n "Firmicutes"
Do you have an idea to get a correct Genbank file?
Thanks
I am trying to convert gff fasta to GenBank. but got following error:
The default organism name 'cellular organisms' is used.
Creating GFF database (gffutils) for chr01.1
Traceback (most recent call last):
File "/HOPS/hqkalsan/python3.9_new/bin/emapper2gbk", line 33, in
sys.exit(load_entry_point('emapper2gbk==0.3.0', 'console_scripts', 'emapper2gbk')())
File "/HOPS/hqkalsan/python3.9_new/lib64/python3.9/site-packages/emapper2gbk-0.3.0-py3.9.egg/emapper2gbk/main.py", line 306, in cli
gbk_creation(nucleic_fasta=args.fastanucleic, protein_fasta=args.fastaprot, annot=args.annotation, gff=args.gff, gff_type=gff_type,
File "/HOPS/hqkalsan/python3.9_new/lib64/python3.9/site-packages/emapper2gbk-0.3.0-py3.9.egg/emapper2gbk/emapper2gbk.py", line 84, in gbk_creation
gbk_result = genomes_to_gbk.gff_to_gbk(nucleic_fasta=nucleic_fasta, protein_fasta=protein_fasta, annot=annot,
File "/HOPS/hqkalsan/python3.9_new/lib64/python3.9/site-packages/emapper2gbk-0.3.0-py3.9.egg/emapper2gbk/genomes_to_gbk.py", line 164, in gff_to_gbk
annot = dict(read_annotation(annot))
File "/HOPS/hqkalsan/python3.9_new/lib64/python3.9/site-packages/emapper2gbk-0.3.0-py3.9.egg/emapper2gbk/utils.py", line 427, in read_annotation
for key in annotation_dict:
UnboundLocalError: local variable 'annotation_dict' referenced before assignment
emapper2gbk genomes -fn genome_dir/chr01.1.fna -fp protein_sequence/chr01.1.faa -o hop_pseudomolecules_v1.1_p1_p2.gbk -g gff/chr01.1.gff -a annotation/chr01.1.tsv
the gff file looks like :
chr01.1 PGSBv3.1.1 gene 29309 31323 0.000 + . ID=id1
chr01.1 PGSBv3.1.1 CDS 29309 31323 . + . ID=id1.1;Parent=id1;primary=T
hello,
We encountered this KeyError while running emapper2gbk. It seems like due to unmatched column for input annotation file from emapper. We tested then with GitHub example files: betbox fna,faa and annotation, but the problem persisted.
We used emapper version 2.1.6 with a default outformat 6 (--outfmt 6).
And we also noticed that online file of go-basic.obo has a missing ":" .
thanks a lot
emapper2gbk genes -fn nucleotide_sequence/ -fp protein_sequence/ -a annotation/ -o gbk/ -go /data/eggnog-mapper_database/eggnog-mapper/data/go-basic.obo
The default organism name 'metagenome' is used.
Assembling Genbank informations for MAG001
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/genes_to_gbk.py", line 103, in faa_to_gbk
create_genbank(gene_nucleic_seqs, gene_protein_seqs, annot, go_namespaces, go_alternatives, output_path, species_informations)
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/genes_to_gbk.py", line 127, in create_genbank
record = record_info(gene_nucleic_id, gene_nucleic_seqs[gene_nucleic_id], species_informations)
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/utils.py", line 298, in record_info
description=species_informations['description'],
KeyError: 'description'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/anaconda3/envs/m2m/bin/emapper2gbk", line 8, in <module>
sys.exit(cli())
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/__main__.py", line 309, in cli
gbk_creation(nucleic_fasta=args.fastanucleic, protein_fasta=args.fastaprot, annot=args.annotation, org=orgnames,
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/emapper2gbk.py", line 196, in gbk_creation
gbk_results = gbk_pool.starmap(genes_to_gbk.faa_to_gbk, multiprocess_data)
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 372, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
KeyError: 'description'
Running emapper2gbk in genes mode with gene identifiers consisting of numbers does not create all the GBK features (translation etc.). There is no crash, a gbk is created but it lacks some important information.
emapper2gbk genes -fn bin.fna -fp bin.faa -o bin.gbk -n "Prevotella" -a bin.tsv
LOCUS _10007119 3225 bp DNA BCT 08-MAR-2022
DEFINITION Prevotella genome.
ACCESSION 10007119
VERSION 10007119
KEYWORDS Prevotella.
SOURCE .
ORGANISM Prevotella
Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae.
FEATURES Location/Qualifiers
source 1..3225
/scaffold="10007119"
/db_xref="taxon:838"
gene 2..3225
/locus_tag="gene_10007119"
CDS 2..3225
/locus_tag="gene_10007119"
ORIGIN
1 atgaaagatc aaaatattaa gaaggtgttg ctcctcggct ccggtgcgtt gaagatcggt
61 gaggccggcg agttcgacta ttccggttca caggcactca aggcgctgcg tgaggaaggc
121 gtctacacgg tgctcatcaa tcctaatatc gccaccgtgc agacctccga gggcgtggcc
[...]
//
When adding a prefix to all identifiers, a correct gbk is created:
LOCUS g10007119 3225 bp DNA BCT 08-MAR-2022
DEFINITION Prevotella genome.
ACCESSION g10007119
VERSION g10007119
KEYWORDS Prevotella.
SOURCE .
ORGANISM Prevotella
Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae.
FEATURES Location/Qualifiers
source 1..3225
/scaffold="g10007119"
/db_xref="taxon:838"
gene 2..3225
/locus_tag="g10007119"
CDS 2..3225
/locus_tag="g10007119"
/gene="carB"
/EC_number="6.3.5.5"
/dbxref="KEGG:R00256"
/dbxref="KEGG:R00575"
/dbxref="KEGG:R01395"
/dbxref="KEGG:R10948"
/dbxref="KEGG:R10949"
/translation="MKDQNIKKVLLLGSGALKIGEAGEFDYSGSQALKALREEGVYTVL
INPNIATVQTSEGVADQIYFLP[...]"
ORIGIN
1 atgaaagatc aaaatattaa gaaggtgttg ctcctcggct ccggtgcgtt gaagatcggt
61 gaggccggcg agttcgacta ttccggttca caggcactca aggcgctgcg tgaggaaggc
121 gtctacacgg tgctcatcaa tcctaatatc gccaccgtgc agacctccga gggcgtggcc
[...]
\\
Hi, I'm trying to use your tool with my output from eggnog-mapper v2
I used your test data and it worked, but not with mine.
emapper2gbk genomic -fg ../Roseburia_inulinivorans_DSM16841/GCF_000174195.1_ASM17419v1_cds_from_genomic.fna -fp ../Roseburia_inulinivorans_DSM16841/GCF_000174195.1_ASM17419v1_protein.faa -o teste.out -a Roseburia_inulinivorans_DSM16841.emapper.annotations
The default organism name 'cellular organisms' is used.
Formatting fasta and annotation file for GCF_000174195.1_ASM17419v1_genomic
Traceback (most recent call last):
File "/raeslab/scratch/lucmac/miniconda3/bin/emapper2gbk", line 8, in <module>
sys.exit(cli())
File "/raeslab/scratch/lucmac/miniconda3/lib/python3.8/site-packages/emapper2gbk/__main__.py", line 245, in cli
gbk_creation(genome=args.fastagenome, proteome=args.fastaprot, annot=args.annotation, gff=args.gff, org=orgnames, gbk=args.out, gobasic=args.gobasic, dirmode=directory_mode, cpu=args.cpu, metagenomic_mode=False)
File "/raeslab/scratch/lucmac/miniconda3/lib/python3.8/site-packages/emapper2gbk/emapper2gbk.py", line 32, in gbk_creation
fa_to_gbk.main(genome, proteome, annot, org, gbk, gobasic)
File "/raeslab/scratch/lucmac/miniconda3/lib/python3.8/site-packages/emapper2gbk/fa_to_gbk.py", line 170, in main
faa_to_gbk(genome_fasta, prot_fasta, annot_table, species_name, gbk_out, gobasic)
File "/raeslab/scratch/lucmac/miniconda3/lib/python3.8/site-packages/emapper2gbk/fa_to_gbk.py", line 64, in faa_to_gbk
annotation_data = dict(read_annotation(annotation_data))
File "/raeslab/scratch/lucmac/miniconda3/lib/python3.8/site-packages/emapper2gbk/utils.py", line 269, in read_annotation
annotation_data.columns = headers_row
File "/home/lucmac/.local/lib/python3.8/site-packages/pandas/core/generic.py", line 5475, in __setattr__
return object.__setattr__(self, name, value)
File "pandas/_libs/properties.pyx", line 66, in pandas._libs.properties.AxisProperty.__set__
File "/home/lucmac/.local/lib/python3.8/site-packages/pandas/core/generic.py", line 669, in _set_axis
self._mgr.set_axis(axis, labels)
File "/home/lucmac/.local/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 220, in set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 24 elements, new values have 1 elements
# Fri Feb 12 12:56:02 2021
# emapper-2.0.6
# emapper.py -i Roseburia_inulinivorans_DSM16841/GCF_000174195.1_ASM17419v1_protein.faa --cpu 4 --itype proteins -m diamond --output_dir eggnog --output Roseburia_inulinivorans_DSM16841
#
#query_name seed_eggNOG_ortholog seed_ortholog_evalue seed_ortholog_score eggNOG OGs narr_og_name narr_og_cat narr_og_desc best_og_name best_og_cat best_og_desc Preferred_name GOs EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction PFAMs
I am trying to convert the eggnogg-mapper output into gbk files. When entering using folders eggnog_fnas,eggnog_faas,eggnog_annot,eggnog_gff, and a namefile.txt, I keep getting a no corresponding protein ID error and then the gbk file isn't made
my command:
emapper2gbk genomes -fn /mnt/d/eggnog_fnas -fp /mnt/d/eggnog_faas -o /mnt/d/gbk_files -g /mnt/d/eggnog_gffs -gt cds_only -go /mnt/d/GO_annotations/go-basic.obo -nf /mnt/d/namefile.txt -a /mnt/d/eggnog_annot -c 2 --keep-gff-annotation
The reply:
Creating GFF database (gffutils) for bin.8
Creating GFF database (gffutils) for bin.5
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.5.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.5.faa (-fp/protein_fasta) sequence for bin.5
Creating GFF database (gffutils) for bin.6
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.8.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.8.faa (-fp/protein_fasta) sequence for bin.8
Creating GFF database (gffutils) for bin.4
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.6.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.6.faa (-fp/protein_fasta) sequence for bin.6
Creating GFF database (gffutils) for bin.7
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.4.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.4.faa (-fp/protein_fasta) sequence for bin.4
Creating GFF database (gffutils) for bin.2
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.7.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.7.faa (-fp/protein_fasta) sequence for bin.7
Creating GFF database (gffutils) for bin.1
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.2.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.2.faa (-fp/protein_fasta) sequence for bin.2
Creating GFF database (gffutils) for bin.3
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.1.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.1.faa (-fp/protein_fasta) sequence for bin.1
No corresponding protein ID between GFF /mnt/d/eggnog_gffs/bin.3.gff (-g/gff) and Fasta protein /mnt/d/eggnog_faas/bin.3.faa (-fp/protein_fasta) sequence for bin.3
/!\ Only 0 on 8 genbanks have been created, check the logs for error.
--- Total runtime 46.52 seconds ---
I am a little confused. When I look at the .gff file, I see a header like thus:
NODE_27_length_174714_cov_8.012086
And when I look in the .faa file, I see this kind of header:
>NODE_27_length_174714_cov_8.012086_1
Is that the problem? How would I fix this?
Thank you for reading!
Hello, I'm trying to use Metage2Metabo with eggNOG output and MAG bins from metaWRAP, but I didn't get a .faa file when running eggNOG. It appears that eggNOG v2 no longer needs to make a .faa file in order to annotate bins.
I'm curious, is there a way I can use those two outputs -- metaWRAP && eggNOG -- without those .faa files? And if not, is there an alternative method of creating a .faa file?
Thank you for your help.
Hi,
I am trying to convert my emapper annotations into genebank format using your tool. I have the following directories set up:
ANNOTATION/ FASTAPROT/ FASTNUCLEIC/ GENBANK/ GFF/ HITS/ ORTHOLOGS/
(emapper2gbk) [mjensen2$] ls FASTNUCLEIC/
BC-1_bin.100.fna BC-1_bin.116.fna BC-1_bin.14.fna etc.
(emapper2gbk) [mjensen2$] ls FASTAPROT/
BC-1_bin.100.emapper.genepred.faa BC-1_bin.116.emapper.genepred.faa BC-1_bin.14.emapper.genepred.faa etc.
(emapper2gbk) [mjensen2$] ls ANNOTATION/
BC-1_bin.100.emapper.annotations BC-1_bin.116.emapper.annotations BC-1_bin.14.emapper.annotations etc.
When I run the following command, however, I get the an error saying that the genomes names do not match the annotation names.
(emapper2gbk) [mjensen2$] emapper2gbk genes -fn ./FASTNUCLEIC/ -fp ./FASTAPROT/ -o ./GENBANK/ -a ./ANNOTATION/ -c 10 -n BC-1 -go gobasic -g ./GFF/
Since it is not the filenames I checked the file content and noticed that emapper has added an additional number to the identifier when it predicted genes and annotated these, e.g.
Contig ID: >bin.1.fak127_1021
Prot ID: >bin.1.fak127_1021_1
Annotation ID: bin.1.fak127_1021_1
I believe this is the problem but I don't know how to work around this as this is something emapper added. Have you encountered this before? I might just be missing a flag of some sort but I am unsure and would appreciate your help!
Cheers,
Marlene
With some macOS system (but not all), there is an issue with the multiprocessing part of emapper2gbk.
This leads to error like:
+[__NSPlaceholderDate initialize] may have been in progress in another thread when fork() was called.
For GitHub Actions, this lead to macOS job reaching time limit without completing.
The fix is to use the OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES before the python call, like:
OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES python test_emapper2gbk.py
Solution from: https://stackoverflow.com/a/52230415
I am using M2M, and I am trying to make gbk files using emapper2gbk for ~1200 bacterial species for use as input in m2m recon. I have created separate folders with .faa, .fna, .gff, and eggNOG files (in .tsv), and have also made a .tsv file with genome ID in column 1 against bacterial name in column 2 for -nf. However, when I try to run emapper using the genomes mode for all of my ~1200 bacterial species, I attain the error attached below. Please note that I have tried to run emapper genomes for each bacteria separately and it was working; the issue seems to be when I try to run it in bulk.
Here is how the organism name .tsv file looks like:
Some versions of eggnog-mapper (but I do not know which) can return multiple matches for the same protein. This could lead to an error in the script (here).
There are multiple solutions:
annotation_data = annotation_data.sort_values('score', ascending=True).drop_duplicates('query').sort_index()annotation_data = annotation_data.groupby(['query']).agg(lambda col: ','.join(col)).reset_index()hello,
We encountered this KeyError while running emapper2gbk. It seems like due to unmatched column for input annotation file from emapper.
We used emapper version 2.1.6 with a default outformat 6 (--outfmt 6)
And we also noticed that online file of go-basic.obo has a missing ":" .
thanks a lot
emapper2gbk genes -fn nucleotide_sequence/ -fp protein_sequence/ -a annotation/ -o gbk/ -go /data/eggnog-mapper_database/eggnog-mapper/data/go-basic.obo
The default organism name 'metagenome' is used.
Assembling Genbank informations for MAG001
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/genes_to_gbk.py", line 103, in faa_to_gbk
create_genbank(gene_nucleic_seqs, gene_protein_seqs, annot, go_namespaces, go_alternatives, output_path, species_informations)
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/genes_to_gbk.py", line 127, in create_genbank
record = record_info(gene_nucleic_id, gene_nucleic_seqs[gene_nucleic_id], species_informations)
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/utils.py", line 298, in record_info
description=species_informations['description'],
KeyError: 'description'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/anaconda3/envs/m2m/bin/emapper2gbk", line 8, in <module>
sys.exit(cli())
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/__main__.py", line 309, in cli
gbk_creation(nucleic_fasta=args.fastanucleic, protein_fasta=args.fastaprot, annot=args.annotation, org=orgnames,
File "/home/anaconda3/envs/m2m/lib/python3.9/site-packages/emapper2gbk/emapper2gbk.py", line 196, in gbk_creation
gbk_results = gbk_pool.starmap(genes_to_gbk.faa_to_gbk, multiprocess_data)
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 372, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
File "/home/anaconda3/envs/m2m/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
KeyError: 'description'
If you try to use emapper2gbk with the new go-basic.obo file there is an error with pronto. Pronto will return the following error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.6/dist-packages/pronto/ontology.py", line 283, in __init__
cls(self).parse_from(_handle) # type: ignore
File "/usr/local/lib/python3.6/dist-packages/pronto/parsers/obo.py", line 45, in parse_from
raise SyntaxError(s.args[0], location) from None
File "http://purl.obolibrary.org/obo/go/snapshot/go.obo", line 436334
def: "Catalysis of the reaction: behenoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxotetracosanoyl-CoA. + carbon dioxide + coenzyme A." [GOC:pz, Rhea: 36507]␊
^
SyntaxError: expected QuotedString
This is linked to an issue in the current go-basic.obo file (format-version: 1.2, data-version: releases/2021-06-16) due to the space in Rhea: 36507. The issue has been fixed in geneontology/go-ontology@104252c. Before the fix is released in the new version of go-basic.obo you can either download the current go-basic.obo (which can be downloaded at this address: http://purl.obolibrary.org/obo/go/go-basic.obo) and manually corrects the Rhea ID (which is associated to the GO Term GO:0102338). Or you can use an old version of go-basic.obo like the one in the test folder of emapper2gbk.
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