Broccoli

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No phylogenies after step 2

1

Hi, I'm trying to run on the example dataset using the command `python ~/Broccoli/broccoli.py -dir ~/Broccoli/example_dataset/ -ext '.fasta'` with diamond version 4.0.515 and fasttree version 2.1.11 but am getting completely...

JesseGibson

What does nb_reduced_prot means ?

2

Hello, Thank you for the tool, Can you explain me what does the column nb_reduced_prot corresponds to in dir_step3/statistics_per_OG.txt please ? Thank you, V

vpymerel

Hello! We've tried to run broccoli with different ratio_ortho values: 0.5 (default), 0.3 and 0.7. It turned out that the results were IDENTICAL for all the values. Is this expected?...

V-JJ

Good morning! I tried to run your software. Everything seems to be ok. However I found that there are some proteins (few cases) that have been assigned twice, to different...

V-JJ

Hi! I'm interested in using Broccoli to analyze ~200 proteomes. The amount of time it takes is considerable (as expected). Would it be a correct use of Broccoli to use...

dirostri

Stuck?

3

Hi, It's days that Broccoli is running like this during step 3:  Why is that? Thanks F

francicco

Run failing at step2

5

Hello I am trying to run Broccoli and it keeps returning the following error message: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/data/evassvis/software/anaconda3/envs/broccoli_env/lib/python3.6/multiprocessing/pool.py", line 119, in worker result =...

MattGoulty

User-defined blast directory?

2

Dear Dr. Derelle, Thank you for your work with Broccoli. Quick question, is there support for a user-supplied blast directory, like `orthofinder -b`? I'd like to port my orthology pipelines...

LovellHAGSC

Python 3.8 global variable not defined

2

When I attempted to run Broccoli with Python 3.8 I got this error: `Traceback (most recent call last): File "broccoli.py", line 145, in broccoli_step1.step1_kmer_clustering(directory, extension, length_kmer, min_aa, nb_threads) File "/Users/5tl/Downloads/Broccoli-1.2/scripts/broccoli_step1.py",...

tlawrence3

issue with files alis_*phy

3

Hi there, I am running Broccoli with an expanded dataset (around 3000 multifasta files from bacteria) as input. The expanded dataset containd a subset that I have used before as...

sguir