Andrey Rozenberg

See working example on [shinyapps](https://har-wradim.shinyapps.io/ggplotgui/).

This seems to be an issue with GSNAP as well. Can the fix now be considered well-tested? Are there plans to merge it with master?

Two years later (v. 3.3.0): the `scripts` directory is available in the conda environment but the scripts are not in the `$PATH`, so one has to use them as `$CONDA_PREFIX/scripts/splitfasta.pl`....

My workflow is to create a separate text file connecting the a3m headers with the a3m file indexes in ffindex: ````python ffdata_file = "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata", ffindex_file = "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex" output_file = "bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_names.txt"...

See [15](15), in particular [this comment](15#issuecomment-471309023).

For conversion to gff, see [jiffy-infernal-hmmer-scripts](https://github.com/nawrockie/jiffy-infernal-hmmer-scripts), in particular infernal-tblout2gff.pl

agat does not crash but the translation is incorrect: ``` $ agat_sp_extract_sequences.pl -g genome.gff -f genome.fna -t cds -p -o genome.faa $ seqkit grep -rp BM212_RS11370 genome.faa >gene-BM212_RS11370 gene=nbis-gene-2141 seq_id=NZ_FOSJ01000070.1...

The issue is that the script is called `download_eggnog_data.py` and not `download_eggnog_database.py`. Pre-downloading the data with `download_eggnog_data.py` avoids the error (and is more flexible in a pipeline context).

@KatharinaHoff Just to support @JohnUrban 's observations: I get the same set of errors in GeneMark.stderr even when using hisat2 (v.2.2.1) instead of STAR. I have a mixture of single-end...

Having the same issue under conda (funannotate=1.8.15) with `--busco_db eukaryota`.