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Yasas1994 / phage_contig_annotator

Annotates genes on putative phage contigs with protein orthologous groups using PHROGs
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Error with "phage_contig_annotator download_db" #2

Closed timeresistance1996 closed 4 months ago

timeresistance1996 commented 5 months ago

Hi @Yasas1994 ,

Thank you for your code. I received an error when i try with  "phage_contig_annotator download_db",

Traceback (most recent call last): File "/root/anaconda3/envs/eggnog/bin/phage_contig_annotator", line 5, in from cli import main File "/root/anaconda3/envs/eggnog/lib/python3.10/site-packages/cli.py", line 6, in from utils import * #call_genes, search_hmms, search_hmms_hhsuite, parse_hmmsearch, generate_plots_and_gff, run_combine File "/root/anaconda3/envs/eggnog/lib/python3.10/site-packages/utils.py", line 26, in from BCBio import GFF ModuleNotFoundError: No module named 'BCBio'

I checked my conda list and bcbio-gff has been downloaded successfully.

Name Version Build Channel

bcbio-gff 0.7.1 pyh7cba7a3_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda

How can i solve this problem？

Yasas1994 commented 5 months ago

Hi @timeresistance1996,

Thanks for reporting this issue. I will test it and get back to you.

Best, Yasas

On Wed, May 8, 2024 at 10:27 AM timeresistance1996 @.***> wrote:

Hi @Yasas1994 https://github.com/Yasas1994 ,

Thank you for your code. I received an error when i try with "phage_contig_annotator download_db",

Traceback (most recent call last): File "/root/anaconda3/envs/eggnog/bin/phage_contig_annotator", line 5, in from cli import main File "/root/anaconda3/envs/eggnog/lib/python3.10/site-packages/cli.py", line 6, in from utils import * #call_genes, search_hmms, search_hmms_hhsuite, parse_hmmsearch, generate_plots_and_gff, run_combine File "/root/anaconda3/envs/eggnog/lib/python3.10/site-packages/utils.py", line 26, in from BCBio import GFF ModuleNotFoundError: No module named 'BCBio'

I checked my conda list and bcbio-gff has been downloaded successfully. Name Version Build Channel

bcbio-gff 0.7.1 pyh7cba7a3_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda

How can i solve this problem？

— Reply to this email directly, view it on GitHub https://github.com/Yasas1994/phage_contig_annotator/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIESWV2NECNCGQJX6FYNAGDZBHOX3AVCNFSM6AAAAABHMPZUYCVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DKMBQGQ2TOOI . You are receiving this because you were mentioned.Message ID: @.***>

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Yasas Wijesekara Doctoral research fellow

Institute for Bioinformatics University Medicine Greifswald Felix-Hausdorff-Str. 8 17475 Greifswald E-mail: @.*** Mobile: +49 (0)15257645870

Yasas1994 commented 5 months ago

I just did a fresh install and everything works just fine. Did you set up the conda environment using the environment.txt file provided within the repository?

timeresistance1996 commented 4 months ago

Hi @Yasas1994 ,

Thank you for your response.

I've tried numerous attempts, but unfortunately, I still encountered failures. It may be due to my configuration. Ultimately, I've decided to utilize BLASTn against .fasta file.