PEPPAN

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Hello, I have checked the files, in order to find out the names of the genes, as Roary or Panaroo presented, however I could not fine the gene annotation? Is...

clin86

BrokenPipeError: [Errno 32] Broken pipe

1

Hi, I was running PEPPAN on ~1700 E. coli genomes. I met an error as follows: Traceback (most recent call last): File "/home/LL/miniconda3/envs/PEPPAN/bin/PEPPAN", line 8, in sys.exit(ortho()) ^^^^^^^ File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/site-packages/PEPPAN/PEPPAN.py",...

verylili

Hi, Professor Zhou, I have installed PEPPAN following the instructions on GitHub. However, I encountered an error while running the example files. The error message is as follows: FileNotFoundError: AttributeError:...

JoyLiu19

Hellow, there are something wrong when I am running PEPPAN_parser. Here is the error log:  However I still got some outputs from PEPPAN_parser even most of them had some...

quliping

**Describe the bug** PEPPAN fails with `"UnboundLocalError: local variable 'name' referenced before assignment"` **To Reproduce** 1) Install PEPPAN ```bash # install via conda conda config --add channels defaults conda config...

MrTomRod

uberBlast.py / parseDiamond: FileNotFoundError

1

I get this error message: ```text $ PEPPAN --testunit $ PEPPAN_parser -g examples/ST131.PEPPAN.gff -s examples/PEPPAN_out -t -c -a 95 (...) 2023-02-21 15:11:25.606204 Run BLASTn starts 2023-02-21 15:11:28.556587 Run BLASTn finishes....

MrTomRod

Output explanations

4

Hello, thank you for great tool! I wonder what mean the output locus tag names in *.PEPPAN.gene_content.Rtab file for example LBv2v5_001134/12 -The LBv2v5_001134 is a locus tag name but the...

ConstantinV

Error with PEPPAN_parser related to the captured group

2

Hello, Thanks for this free software. I ran `PEPPAN 1.0.6` successfully, but when I try to run the parser I got the following error, related to the captured group: `PEPPAN_parser...

matrs

Failed to mmap memory dataSize=0 File=./NS_eyo9ogxk/seq.db_h. Error 22.

1

Hello, I am new to using these tools, so please excuse me if I don't explain well. I am trying to create a pangenome of Borrelia spp to map my...

ghost

I am having some problems running the command given to test PEPPAN: `PEPPAN -p examples/ST131 -P examples/GCF_000010485.combined.gff.gz examples/*.gff.gz` I get an error message: > 2021-06-25 15:52:46.357579 COMMAND: /home/idowuol/anaconda3/bin/PEPPAN -p examples/ST131...

Tj-Idowu