RFPlasmid

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First of all thank you for your wonderful software! I ve been trying to run it on MAGs from metagenomes on a slurm server. Installation was done with conda and...

sapuizait

Warning while installing with conda

1

Hi, I runned into a warning while installing the tool thru conda. The tool still runs well, but it gives an error message when integrating into a pipeline. Error message...

jpaganini

Merge error

1

Greetings I get the following error (installed via conda): Create df_files ; done Traceback (most recent call last): File "/home/user/Data/miniconda3/envs/rfplasmid/lib/python3.7/site-packages/RFPlasmid/rfplasmid.py", line 346, in df1 = pd.merge(df1a, df1b, how='right', left_on=['genome','contig'], right_on=['genome','contig'])...

VMJarocki

# character cannot be added to input files name

1

**Incomplete output when file names contain the '#' character. The only output obtained is the outputdataframe.csv.** Example of file names: 30345_1#218_illumina.fasta 30348_2#44_illumina.fasta **When replacing '#' with '_' in the file...

jpaganini

Often files have the .fna extension. We should recognize these as well as valid sequence files

aldertzomer

rfplasmid in a docker container errors during `rfplasmid --initialize`

1

Hello, I am trying to wrap RFPlasmid in a docker container, and I am installing it using conda. When I run the installation step, everything seems to run well. Then...

juliofdiaz

python=3.10 issue with split() function

7

My newest conda environment with rfplasmid pulled python=3.10 which gave me this error: ``` Finished processing 1 of 1 (100.00%) bins. Finished parsing hits for 1 of 1 (100.00%) bins....

aschuerch

Training on complete plasmids?

1

Hello, I am interested in running RFPlasmid on an Enterobacteriaceae dataset and I see there is a precomputed database for it. However, I am wondering whether it would not be...

cizydorczyk

file is too short for prediction?

1

Hi again Sorry for the multiple threads but there are 2 different issues. This is sth that prevents me from running the software. I am trying to run rfplasmid on...

sapuizait

Hi there I would like to run the rfplasmid on E.coli genomes. I saw you mention them but i cannot find a model. Is it an upcoming feature or is...

sapuizait