database building error

[yye88]

[13:34:17] ERROR - File parsing failed, exiting... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/share/apps/miniconda/anaconda3-2019.10/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, **kwds)) File "/home/yye/.local/lib/python3.7/site-packages/cblaster/genome_parsers.py", line 209, in parse_file for record in function() File "/home/yye/.local/lib/python3.7/site-packages/cblaster/genome_parsers.py", line 162, in parse_gff [*gene, *merge_cds_features(cds)], File "/home/yye/.local/lib/python3.7/site-packages/cblaster/genome_parsers.py", line 113, in merge_cds_features if merged[-1].qualifiers["ID"][0] == feature.qualifiers["ID"][0]: KeyError: 'ID' """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/yye/.local/lib/python3.7/site-packages/cblaster/database.py", line 204, in makedb for organism in pool.imap(func, group): File "/share/apps/miniconda/anaconda3-2019.10/lib/python3.7/multiprocessing/pool.py", line 748, in next raise value KeyError: 'ID' [13:34:17] INFO - Writing FASTA to myDb.fasta [13:34:17] INFO - Building DIAMOND database at myDb.dmnd [13:34:17] INFO - Done!

[gamcil]

Would you be able to upload any of the files you are trying to build a database from?

[yye88]

DF.zip Thank you for reply. I upload a zip file containing a gff file and a coresponding fasta file. Please hava a look what went wrong. Thank you.

[gamcil]

It looks like the GFF3 produced by Augustus is missing some required fields. From a quick search, I think this is a well known issue with Augustus (https://github.com/Gaius-Augustus/Augustus/issues/74). One suggestion from that link is to use agat_sp_gxf_to_gff3.pl from AGAT (https://github.com/NBISweden/AGAT) - maybe that can fix your GFF3 file?

[yye88]

Thank you so much, I will try that for sure.