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fwhelan / coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
GNU General Public License v3.0
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Error in using coinfinder #32

Closed vigneshlab closed 4 years ago

vigneshlab commented 4 years ago

Hi, I installed coinfinder using conda.

Typing coinfinder on the terminal gives the following:

CoinFinder 1.1 RELEASE BUILD @ Oct 7 2020 12:06:08. Please see readme.md for details.

I downloaded the dataset from https://github.com/fwhelan/coinfinder-manuscript and when I try use the gene-presence-absence.csv file, it throws up the following error:

$coinfinder -I gene_presence_absence.csv Reading arguments...

CORRECTION ······· = FRACTION (special) METHOD ··········· = COINCIDENCE ALT_HYPOTHESIS ··· = GREATER MAX_MODE ········· = ACCOMPANY SET_MODE ········· = FULL PERMIT_FILTER ···· = YES VERBOSE ·········· = YES OUTPUT_ALL ······· = NO terminate called after throwing an instance of 'std::logic_error' what(): Cutoff mode specified when method != CONNECTIVITY. Aborted (core dumped)

Could you please help resolve the issue?

noahaus commented 4 years ago

Hi, I recently ran coinfinder and noticed that there may be an error in how you called your command. try following this syntax and it may work?

 coinfinder -i mbovis_prab.csv -I -p core_gene.collapsed.tre -o mbov_pan.coin
vigneshlab commented 4 years ago

Thank you! It works now!

vigneshlab commented 4 years ago

I tried to use the tab-limited input format suggested in the readme file. When I use the example given in the readme file, it works fine. However, when I add a few more lines (gene 4) such as below, I get error (mentioned below):

gene_1 genome_1 gene_1 genome_2 gene_1 genome_3 gene_2 genome_2 gene_2 genome_3 gene_3 genome_1 gene_3 genome_2 gene_4 genome_1 gene_4 genome_2 gene_4 genome_3

$coinfinder -i gene.txt -a

Reading arguments...

CORRECTION ······· = BONFERRONI METHOD ··········· = COINCIDENCE ALT_HYPOTHESIS ··· = GREATER MAX_MODE ········· = ACCOMPANY SET_MODE ········· = FULL PERMIT_FILTER ···· = NO VERBOSE ·········· = NO OUTPUT_ALL ······· = NO FRACTION CUTOFF ·· = N/A SIGNIFICANCE_LEVEL = 0.05 COMBINED_FILE ···· = gene.txt GENE_NAME ······· = Genes GENOME_NAME ········ = Genomes

You have not provided a phylogeny. This is okay, coinfinder works just fine without a phylogeny. The steps involving the detection of lineage dependent elements will be skipped.

Please be aware that coinfinder will generate a mock phylogeny for the purposes of data presentation in the output heatmaps.

Press any key to accept and continue or Ctrl+C to quit.

Formating input into gene_p_a for input into coinfinder... ERROR MESSAGE FROM Python: Traceback (most recent call last): File "/opt/miniconda3/bin//coinfind-code/create_roary.py", line 68, in gen = (line.split("\t")[1]).strip() IndexError: list index out of range

Please help. Thanks.

fwhelan commented 4 years ago

Hi vigneshlab,

It looks like your modifications to the gene.txt file might not keep to the genegenome format? I usually check this in vim using :set list though there are many ways!

Let me know if that helps!

vigneshlab commented 4 years ago

Hi vigneshlab,

It looks like your modifications to the gene.txt file might not keep to the genegenome format? I usually check this in vim using :set list though there are many ways!

Let me know if that helps!

Thanks fwhelan. It helped. There were issues with the format. vim set list was useful. :+1: