inquiry on error

[LanSabb]

Hi

I installed the cblaster and attempted to build the local DB with the following code

mamba create -y -n cblaster cblaster=1.3.20 ; conda activate cblaster

(Input folder contains 14 genome sequences and prodigal-computed GFF files) conda activate cblaster cblaster makedb -n DB $In/*.gff conda deactivate ;

The following error prevents the further analysis. Do you have any idea to resolve it ? Is it due to python version issue??

Importing genomicsqlite failed, falling back to SQLite3 [20:38:13] INFO - Starting makedb module [20:38:13] INFO - Initialising cblaster SQLite3 database to DB.sqlite3 [20:38:13] INFO - Parsing 14 genome files, in 1 batches of 14 [20:38:13] INFO - Processing batch 1 [20:38:13] INFO - 2606217604.gff [20:38:13] INFO - FO000002.1.gff [20:38:13] INFO - GCA_001313145.1.gff [20:38:13] INFO - GCA_001996325.1.gff [20:38:13] INFO - GCA_007989485.1.gff [20:38:13] INFO - GCF_000010305.1.gff [20:38:13] INFO - GCF_000013385.1.gff [20:38:13] INFO - GCF_000196135.1.gff [20:38:13] INFO - GCF_000237885.1.gff [20:38:13] INFO - GCF_000621305.1.gff [20:38:13] INFO - GCF_003112695.1.gff [20:38:13] INFO - GCF_012843265.1.gff [20:38:13] INFO - GCF_017310505.1.gff [20:38:13] INFO - GCF_030954495.1.gff [20:38:13] WARNING - Found no CDS features in NZ_BFBP01000019.1 [GCF_003112695.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_AGSL01000108.1 [GCF_000237885.1.gff] [20:38:13] WARNING - Found no CDS features in MQMM01000005.1 [GCA_001996325.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JHYR01000043.1 [GCF_000621305.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_AGSL01000079.1 [GCF_000237885.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000078.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000079.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000080.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000082.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000085.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000086.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000088.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000089.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000091.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000092.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000093.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000094.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000098.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000103.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000104.1 [GCF_012843265.1.gff] [20:38:13] WARNING - Found no CDS features in NZ_JABAIT010000105.1 [GCF_012843265.1.gff] [20:38:14] WARNING - Found no CDS features in BJUR01000138.1 [GCA_007989485.1.gff] [20:38:15] WARNING - Found no CDS features in BBFH01001992.1 [GCA_001313145.1.gff] [20:38:15] INFO - Saving 57002 genes [20:38:16] INFO - Writing FASTA to DB.fasta Traceback (most recent call last): File "/opt/anaconda3/envs/cblaster/bin/cblaster", line 10, in sys.exit(main()) ~~~~^^ File "/opt/anaconda3/envs/cblaster/lib/python3.13/site-packages/cblaster/main.py", line 423, in main database.makedb( ~~~~~~~~~~~~~~~^ args.paths, ^^^^^^^^^^^ ...<3 lines>... force=args.force, ^^^^^^^^^^^^^^^^^ ) ^ File "/opt/anaconda3/envs/cblaster/lib/python3.13/site-packages/cblaster/database.py", line 236, in makedb sqlite_to_fasta(fasta_path, sqlite_path, compress) ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda3/envs/cblaster/lib/python3.13/site-packages/cblaster/database.py", line 76, in sqlite_to_fasta for (record,) in cur.execute(sql.FASTA): ~~~~~~~~~~~^^^^^^^^^^^ sqlite3.OperationalError: no such column: ">" - should this be a string literal in single-quotes?

Thanks!

[OllieMattinson97]

I had the same problem. Downgrading libsqlite from 3.49.1 to 3.48.0 resolved the issue.

[LanSabb]

Thanks for comment !