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Carrion-lab / bacLIFE

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No module named Bio #21

Open ykm7788 opened 2 weeks ago

ykm7788 commented 2 weeks ago

Hiya， When I run snakemake -j 64 --use-conda with example data, I ran into this error:

localrule antismash: input: intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk output: intermediate_files/antismash/Pseudomonas_syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk jobid: 20 reason: Missing output files: intermediate_files/antismash/Pseudomonas_syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk; Input files updated by another job: intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk wildcards: genus=Pseudomonas, species=syringae, str=UMAF1029, replicon=O resources: tmpdir=/tmp

Activating conda environment: antismash_bacLIFE

[Thu Oct 24 12:43:52 2024] Job 7: Executing genbank_to_protein_fasta on the following files intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk. Reason: Missing output files: intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.ext_prot.faa, intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.ext_prot.faa.tags; Input files updated by another job: intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk

Traceback (most recent call last): File "./src/genbank_to_protein_fasta.py", line 3, in import Bio ImportError: No module named Bio [Thu Oct 24 12:43:52 2024] Error in rule extract_proteins: jobid: 7 input: intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk output: intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.ext_prot.faa, intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.ext_prot.faa.tags shell: python ./src/genbank_to_protein_fasta.py --genbank intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk --fasta intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.ext_prot.faa (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I think I have installed Bio package because when I run python -c "import Bio; print(Bio.__version__)" in antismash_bacLIFE environment, it printed 1.78

Also, if I manually run python ./src/genbank_to_protein_fasta.py --genbank intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk --fasta intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.ext_prot.faa, I can get correct output as : Converting :intermediate_files/annot/syringae_UMAF1029_O/Pseudomonas_syringae_UMAF1029_O.gbk Written :1063 sequences from Pseudomonas syringae strain UMAF1029 Written :1161 sequences from Pseudomonas syringae strain UMAF1029 Written :1237 sequences from Pseudomonas syringae strain UMAF1029 Written :1304 sequences from Pseudomonas syringae strain UMAF1029 Written :1373 sequences from Pseudomonas syringae strain UMAF1029 Written :1389 sequences from Pseudomonas syringae strain UMAF1029 Written :1394 sequences from Pseudomonas syringae strain UMAF1029 Written :1397 sequences from Pseudomonas syringae strain UMAF1029 Written :1403 sequences from Pseudomonas syringae strain UMAF1029 Written :1403 sequences from Pseudomonas syringae strain UMAF1029 Written :1403 sequences from Pseudomonas syringae strain UMAF1029 Written :2119 sequences from Pseudomonas syringae strain UMAF1029 Written :2119 sequences from Pseudomonas syringae strain UMAF1029 Written :3533 sequences from Pseudomonas syringae strain UMAF1029 Written :3872 sequences from Pseudomonas syringae strain UMAF1029 Written :4328 sequences from Pseudomonas syringae strain UMAF1029 Written :4627 sequences from Pseudomonas syringae strain UMAF1029 Written :4859 sequences from Pseudomonas syringae strain UMAF1029 Written :5023 sequences from Pseudomonas syringae strain UMAF1029 Written :5190 sequences from Pseudomonas syringae strain UMAF1029

kevinbretscher commented 6 days ago

Hi, sorry for the late reply. Do you still have the issue? One option could be to try to install biopython again in the conda enviroment. Or you could try to delete the conda env and build it again.