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gem-pasteur / PanACoTA

PANgenome with Annotations, COre identification, Tree and corresponding Alignments
GNU Affero General Public License v3.0
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Error while trying to run prokka on #40

Closed aymericola closed 1 year ago

aymericola commented 1 year ago

Hello, I am currently using prokka 1.14.6 with PanACoTA v1.4.0. I tried to use all module on some genomes. Unfortunately, prokka encountered some kind of mistakes . Hence, I tried simpler and simpler commands but nothing worked. So, i tried to run the tutorial example commands on the simplified genomes available on this GitHub. I encountered the same mistake which makes me think that the problem comes from dependencies rather than my genomes or my command lines.

I paste down here the PanACoTA-annotate_list_genomes.log.details

[2023-06-29 16:23:29] :: INFO :: PanACoTA version 1.4.0 [2023-06-29 16:23:29] :: INFO :: Command used PanACoTA annotate -d Examples/genomes_init -r Examples/2-res-prokka -l Examples/input_files/list_genomes.lst -n GENO --l90 3 --nbcont 10 [2023-06-29 16:23:29] :: INFO :: Reading genomes [2023-06-29 16:23:29] :: INFO :: Cutting genomes at each time there are at least 5 'N' in a row, and then, calculating genome size, number of contigs and L90. [2023-06-29 16:23:29] :: INFO :: Generating distribution of L90 and #contigs graphs. [2023-06-29 16:23:30] :: INFO :: -> Original sequences folder ('orig_name' column): Examples/genomes_init [2023-06-29 16:23:30] :: INFO :: -> If original sequence not found in Examples/genomes_init, look for it in Examples/2-res-prokka/tmp_files, as it must be a concatenation of several input sequence files. [2023-06-29 16:23:30] :: INFO :: -> Folder with sequence files that will be used for annotation ('to_annotate' column): Examples/2-res-prokka/tmp_files [2023-06-29 16:23:30] :: INFO :: Renaming kept genomes according to their quality (3 genomes) [2023-06-29 16:23:30] :: INFO :: Annotating all genomes with prokka [2023-06-29 16:23:30] :: DETAIL :: Start annotating GENO.0623.00001 from Examples/2-res-prokka/tmp_files/genome1.fst_prokka-split5N.fna with Prokka [2023-06-29 16:23:30] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-prokka/tmp_files/genome1.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GENO.0623.00001 --centre prokka Examples/2-res-prokka/tmp_files/genome1.fst_prokka-split5N.fna [2023-06-29 16:23:30] :: ERROR :: Error while trying to run prokka on GENO.0623.00001 from Examples/2-res-prokka/tmp_files/genome1.fst_prokka-split5N.fna [2023-06-29 16:23:30] :: DETAIL :: Start annotating GENO.1216.00002 from Examples/2-res-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna with Prokka [2023-06-29 16:23:30] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GENO.1216.00002 --centre prokka Examples/2-res-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna [2023-06-29 16:23:30] :: ERROR :: Error while trying to run prokka on GENO.1216.00002 from Examples/2-res-prokka/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna [2023-06-29 16:23:30] :: DETAIL :: Start annotating GEN4.1111.00001 from Examples/2-res-prokka/tmp_files/genome4.fst_prokka-split5N.fna with Prokka [2023-06-29 16:23:30] :: DETAIL :: Prokka command: prokka --outdir Examples/2-res-prokka/tmp_files/genome4.fst_prokka-split5N.fna-prokkaRes --cpus 1 --prefix GEN4.1111.00001 --centre prokka Examples/2-res-prokka/tmp_files/genome4.fst_prokka-split5N.fna [2023-06-29 16:23:30] :: ERROR :: Error while trying to run prokka on GEN4.1111.00001 from Examples/2-res-prokka/tmp_files/genome4.fst_prokka-split5N.fna [2023-06-29 16:23:30] :: ERROR :: Error: No genome was correctly annotated, no need to format them.

This is a new computer I'm working on, and everythink worked fine on the previous one, with the same versions of prokka & panacota.

If anyone has an idea on how to fix this, I would be very thankfull.

asetGem commented 1 year ago

Hi ! I see that this issue has been closed without any comment. Have you solved your problem with prokka?

aymericola commented 1 year ago

Hello, Yes I solved it. The problem was that the Ubuntu version I had : Focal 20.04.6. Prokka database was not compatible with the software on that version. I updated Ubuntu and hence solved the problem. Best, Aymeric.