Core gene alignment - FileNotFoundError - missing aligned_gene_sequences folder

[djbradshaw2]

Greetings Panaroo Developers,

Thank you very much for such a great tool!

I am running into an error that occurs either when I try to run a core alignment either as part of the panaroo script or separately as a panaroo-msa script. The error states something like: FileNotFoundError: [Errno 2] No such file or directory: 'CG_rep_NCG_no_CY_panaroo_pangenome_merged_paralogs/aligned_gene_sequences/yrbN.aln.fas'. This happens both with the 1.5.2 and 1.6.0 versions of panaroo as well as with mafft or clustal aligners; both panaroo versions were installed with conda.

This seems to be different than that No pangenome alignment in Panaroo output folder #72 issue in that the aligned_gene_sequences folder is not generated...

Please see example scripts below and attached stdout and stderr files.

For some background, I am running panaroo on 9,553 Salmonella Enteritidis gff3 files from bakta via slurm on an HPC with 48 cores and 432Gb. I am running the alignment in order to use it in pyseer. Alternatively, I have generated a mash sketch of the genomes that can be used as the alignment, but I would prefer to use the alignment per your guidance document on using panaroo outputs in pyseer.

Please let me know if you have any questions or if there is any other information you need.

Sincerely,

David

##Scripts ran

#Load environment
source /project/fsepru113/dbradshaw/miniconda3/bin/activate panaroo_1_5_2

#Run the merged paralogs panaroo script
panaroo -i CG_Rep_NCG_Conf_Filt_Enteritidis_WW_111425_gff3_paths.txt -o CG_rep_NCG_no_CY_panaroo_pangenome_merged_paralogs --merge_paralogs --clean-mode strict -t 48 -a core --remove-invalid-genes

#Create a core alignment
panaroo-msa -o CG_rep_NCG_no_CY_panaroo_pangenome_merged_paralogs -t 35 -a core --verbose --aligner mafft

##Files

Please note that $home was used to project identifying information in stdouts and stderrs.

Panaroo stdout:

Rep_Step_4_pangenome_CG_NCG_Conf_Filt_Enteritidis_Worldwide_111425.stdout.txt

Panaroo stderr:

Rep_Step_4_pangenome_CG_NCG_Conf_Filt_Enteritidis_Worldwide_111425.stderr.txt

Panaroo tmp directory:

panaroo_tmp_directory.txt

Panaroo outputs:

panaroo_outputs.txt

Panaroo MSA stderr:

Rep_Step_4b_pangenome_iqtree_mash_pyseer_CG_NCG_Conf_Filt_Enteritidis_Worldwide_111425.stderr.txt

Panaroo MS tmp directory:

panaroo_msa_tmp_directory.txt