UnboundLocalError: local variable 'input_fna_clean' referenced before assignment

[fujch7]

Hi developer, I met the error below. How could I deal with it? Besides, for arguments -d, after first time I ran the command, the database file phylophlan.dmnd was produced. Could I just specified the path of database like /path/phylophlan_databases/phylophlan/phylophlan.dmndfor my next running command? It would be appreciated for your help.

(phylophlan) [root@instance-xvlawteu phylophlan3]# phylophlan -i /home/prodigal/output/0827fna/ --accurate --diversity low -d phylophlan -f supermatrix_aa.cfg -t a --nproc 2 --output_folder /home/phylophlan3/phy_output/ --proteome_extension faa Loading files from "/home/prodigal/output/0827fna" Traceback (most recent call last): File "/root/anaconda3/envs/phylophlan/bin/phylophlan", line 10, in sys.exit(phylophlan_main()) File "/root/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan.py", line 3213, in phylophlan_main standard_phylogeny_reconstruction(project_name, configs, args, db_dna, db_aa) File "/root/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan.py", line 2910, in standard_phylogeny_reconstruction if input_fna_clean: UnboundLocalError: local variable 'input_fna_clean' referenced before assignment

[fujch7]

The above problem occurred after I used the amino sequences in FAA file as input.

If I use genomes as input and use --nproc params, there will be another problems when mapping. see below: _'/home/fujch/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/', 'DBUS_SESSION_BUS_ADDRESS': 'unix:abstract=/tmp/dbus-YtQYAttD9u,guid=bf43da6c507aafd9f4b9dbb25f54b77a', 'LESSOPEN': '||/usr/bin/lesspipe.sh %s', 'CONDA_DEFAULT_ENV': 'phylophlan', 'WINDOWPATH': '1', 'XDG_RUNTIME_DIR': '/run/user/1000', 'DISPLAY': ':0', 'XDG_CURRENT_DESKTOP': 'GNOME-Classic:GNOME', 'COLORTERM': 'truecolor', 'XAUTHORITY': '/root/.xauth3BEJWC'}

[e] Command '['/root/anaconda3/envs/phylophlan/bin/diamond', 'blastx', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', '/mnt/hgfs/share/phylophlan3/output/0827fna_phylophlan/tmp/clean_dna/Aerosticca_soli_Dysh456_T_GCA_003967035.1_genomic.fna', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', '/mnt/hgfs/share/phylophlan3/output/0827fna_phylophlan/tmp/map_dna/Aerosticca_soli_Dysh456_T_GCA_003967035.1_genomic.b6o.bkp']' died with <Signals.SIGABRT: 6>.

[e] error while mapping {'program_name': '/root/anaconda3/envs/phylophlan/bin/diamond', 'params': 'blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0', 'input': '--query', 'database': '--db', 'output': '--out', 'version': 'version', 'command_line': '#program_name# #params# #input# #database# #output#'} /mnt/hgfs/share/phylophlan3/output/0827fna_phylophlan/tmp/clean_dna/Aerosticca_soli_Dysh456_T_GCA_003967035.1_genomic.fna phylophlan_databases/phylophlan/phylophlan.dmnd /mnt/hgfs/share/phylophlan3/output/0827fna_phylophlan/tmp/map_dna Aerosticca_soli_Dysh456_T_GCA_003967035.1_genomic.b6o.bkp False

[e] Command '['/root/anaconda3/envs/phylophlan/bin/diamond', 'blastx', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', '/mnt/hgfs/share/phylophlan3/output/0827fna_phylophlan/tmp/clean_dna/Aerosticca_soli_Dysh456_T_GCA_003967035.1_genomic.fna', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', '/mnt/hgfs/share/phylophlan3/output/0827fna_phylophlan/tmp/map_dna/Aerosticca_soli_Dysh456_T_GCA_003967035.1_genomic.b6o.bkp']' died with <Signals.SIGABRT: 6>.

[e] gene_markersidentification crashed

And I have another question. Whether I use nucleotide or amino acid files as input, phylogenetic trees are based on amino acid sequences as long as parameter --force_nucletides are not used. And I can use --force_nucletides to force the phylogeny tree being built based on nucleotide sequence?

[fasnicar]

Hi,

Can you please provide the version of PhyloPhlAn you're using (--version)?

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For the -d parameter, the next time you should just specify the same -d phylophlan and if you use diamond it will be detected that the indexed version is already present.

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UnboundLocalError: local variable 'input_fna_clean' referenced before assignment

what is the content of the /home/prodigal/output/0827fna/ folder?

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And I have another question. Whether I use nucleotide or amino acid files as input, phylogenetic trees are based on amino acid sequences as long as parameter --force_nucletides are not used. And I can use --force_nucletides to force the phylogeny tree being built based on nucleotide sequence?

If you use --force_nucleotides only input genomes will be used and this is generally used when your inputs are only genomes and the database a set of proteins. If your inputs are a mix of genomes and proteomes then you can only build a phylogeny based on amino acids and so you should not specify the --force_nucleotides parameter.

[fujch7]

1. PhyloPhlAn version 3.0.54 (26 August 2020)
2. /home/prodigal/output/0827fna/ folder contains protein sequences predicted by prodigal (v2.6.3), and the character "" in the output file produced by prodigal has been delete. I know the character "" will cause an error in phylophlan version 1.
3. when inputs are only genomes and the database are proteins, using --force_nucleotideswill make the phylogeny built based on nucleotides sequence. Is it right?

[fasnicar]

Many thanks for the version.

I guess the character is the "_", right? I don't think that should be a problem with the new version of PhyloPhlAn.

For 3, yes, if your inputs are genomes and the database proteins, with --force_nucleotides the phylogeny will be built using nucleotides.

Is your input folder containing also genomes?

[fasnicar]

Hi, this should be fixed with commit d723a3c703f41a361d153949460ba561b9879478. This version is not yet packaged in Bioconda, so you should get the code directly from the repository.

Many thanks, Francesco