Errors during sgt_constructor.py

[thibantoine]

Hello,

I am using version Phylofisher 1.2.13. See attached my 4 input proteomes proteome.tar.gz. I tried to do the workflow on my personal computer. The commands I ran were as follows;

config.py -d ../PhyloFisherDatabase_v1.0/database/ -i input_metadata.tsv
fisher.py -t 20
informant.py -i fisher_out_Jul.10.2024/
working_dataset_constructor.py -i fisher_out_Jul.10.2024/
sgt_constructor.py -i working_dataset_constructor_out_Jul.10.2024/ -t 18

Unfortunately, after several attempts (by changing the starting data or the number of threads) I'm stuck at the "Filter, align, and trim gene files followed by gene tree construction" stage. I get numerous errors such as ;

Error in rule prequal:
    jobid: 442
    output: /home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/prequal/RPO-C.aa.f                                                                                                           iltered
    log: /home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/logs/prequal/RPO-C.lo                                                                                                           g (check log file(s) for error message)
    conda-env: /home/thibault/Nucleomorph_T4/.snakemake/conda/9203e1ffd8a91144bfef87b70196c1                                                                                                           71
    shell:
        prequal /home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/prequal/RPO-C.                                                                                                           aa >/home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/logs/prequal/RPO-C.log 2>/                                                                                                           home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/logs/prequal/RPO-C.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash s                                                                                                           trict mode!)

Error in rule length_filter_mafft:
    jobid: 417
    output: /home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/length_filtration/                                                                                                           mafft/MCM-B.aln
    log: /home/thibault/Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/logs/length_filter_ma                                                                                                           fft/MCM-B.log (check log file(s) for error message)
    conda-env: /home/thibault/Nucleomorph_T4/.snakemake/conda/bed6548f46a2aea955200caef62385                                                                                                           5f
    shell:
        mafft --thread 1 --globalpair --maxiterate 1000 --unalignlevel 0.6 /home/thibault/Nu                                                                                                           cleomorph_T4/sgt_constructor_out_Jul.10.2024/prequal/MCM-B.aa.filtered >/home/thibault/Nucle                                                                                                           omorph_T4/sgt_constructor_out_Jul.10.2024/length_filtration/mafft/MCM-B.aln 2>/home/thibault                                                                                                           /Nucleomorph_T4/sgt_constructor_out_Jul.10.2024/logs/length_filter_mafft/MCM-B.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash s                                                                                                           trict mode!)

Thank you in advance for your help,

Thibault

[atice]

Hi @thibantoine,

Sorry for the delay. I have been out of the office on a collecting trip. Can you provide me with the log files for the sgt_constructory.py run?

[thibantoine]

Hi,

Please find attached the log files logs.tar.gz

Thank you in advance,

Thibault