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Prokka not using default value for --kingdom in Advanced Mode #3

Open hazmup opened 11 months ago

hazmup commented 11 months ago

When I use bacseq in advanced mode, Prokka does not use the default value for --kingdom so I have to set this and --gcode as well. Also, maybe there should be a check so that it cannot run unless a required value is specified, otherwise bacseq is stuck and I have to rerun the whole pipeline. Thank you for your work!

hazmup commented 11 months ago

After specifying both --kingdom and --gcode, Prokka fails with the following output:

--compliant is unchecked
--addgenes is unchecked
--usegenus is unchecked
--rfam is unchecked
--centre
        Option 1:
--genus
        Option 2:
--species
        Option 3:
--kingdom
        Option 4: Bacteria
--gcode
        Option 5: 11
--cpus
        Option 6: 16
/mnt/d/bacseq/Software/biotools/scripts/./prokka_script.sh
[/mnt/d/bacseq/Software/biotools/scripts/./prokka_script.sh, /mnt/d/bacseq, , , , Bacteria, 11, 16,  ,  ,  ,  ]
[10:08:44] This is prokka 1.14.6
[10:08:44] Written by Torsten Seemann <torsten.seemann@gmail.com>
[10:08:44] Homepage is https://github.com/tseemann/prokka
[10:08:44] Local time is Wed Nov 22 10:08:44 2023
[10:08:44] You are micro
[10:08:44] Operating system is linux
[10:08:44] You have BioPerl 1.7.8
Argument "1.7.8" isn't numeric in numeric lt (<) at /home/micro/mambaforge/envs/bacseq/bin/prokka line 259.
[10:08:44] System has 16 cores.
[10:08:44] Will use maximum of 16 cores.
[10:08:44] Annotating as >>> Bacteria <<<
[10:08:44] 'Ab1.scaffolds' is not a readable non-empty FASTA file
cp: cannot stat '/mnt/d/bacseq/Software/output/prokka/Ab1.scaffolds/Ab1.scaffolds.gff': No such file or directory
/mnt/d/bacseq/Software/biotools/scripts/./prokka_script.sh: line 22: cd: /mnt/d/bacseq/Software/output/prokka/Ab1.scaffolds: No such file or directory
sed: can't read Ab1.scaffolds.tsv: No such file or directory
/mnt/d/bacseq/Software/biotools/scripts/./prokka_script.sh: line 25: /mnt/d/bacseq/Software/output/prokka/Ab1.scaffolds/Ab1.scaffolds.html: No such file or directory
[10:08:44] This is prokka 1.14.6
[10:08:44] Written by Torsten Seemann <torsten.seemann@gmail.com>
[10:08:44] Homepage is https://github.com/tseemann/prokka
[10:08:44] Local time is Wed Nov 22 10:08:44 2023
[10:08:44] You are micro
[10:08:44] Operating system is linux
[10:08:44] You have BioPerl 1.7.8
Argument "1.7.8" isn't numeric in numeric lt (<) at /home/micro/mambaforge/envs/bacseq/bin/prokka line 259.
[10:08:44] System has 16 cores.
[10:08:44] Will use maximum of 16 cores.
[10:08:44] Annotating as >>> Bacteria <<<
[10:08:44] 'Ab3.scaffolds' is not a readable non-empty FASTA file
cp: cannot stat '/mnt/d/bacseq/Software/output/prokka/Ab3.scaffolds/Ab3.scaffolds.gff': No such file or directory
/mnt/d/bacseq/Software/biotools/scripts/./prokka_script.sh: line 22: cd: /mnt/d/bacseq/Software/output/prokka/Ab3.scaffolds: No such file or directory
sed: can't read Ab3.scaffolds.tsv: No such file or directory
/mnt/d/bacseq/Software/biotools/scripts/./prokka_script.sh: line 25: /mnt/d/bacseq/Software/output/prokka/Ab3.scaffolds/Ab3.scaffolds.html: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
cat: '/mnt/d/bacseq/Software/output/prokka/*/*.txt': No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
grep: /mnt/d/bacseq/Software/output/prokka/*/*.txt: No such file or directory
cat: '/mnt/d/bacseq/Software/output/prokka/*/*.txt': No such file or directory
Prokka is Successful
The result files are available at: /mnt/d/bacseq/Software/Output/prokka