Empty Output

[kittyBS]

Hello,
I am trying to use the i-ADHoRe tool for human and mouse using the output files from OrthoFinder. For this purpose, I created the blast_table=Orthologs.list file, which looks like:
ENSG00000125498 OG0000000
ENSG00000273510 OG0000000
ENSG00000273517 OG0000000
ENSG00000273578 OG0000000
ENSG00000273603 OG0000000
ENSG00000273661 OG0000000
ENSG00000273794 OG0000000
ENSG00000274406 OG0000000
ENSG00000274412 OG0000000
ENSG00000274438 OG0000000
The iadhore.ini file I used for the analysis is as follows:
genome=Human
ENSG00000000003 query/ENSG00000000003.lst
ENSG00000000005 query/ENSG00000000005.lst
...
genome=Mouse
ENSMUSG00000000001 subject/ENSMUSG00000000001.lst
ENSMUSG00000000003 subject/ENSMUSG00000000003.lst
ENSMUSG00000000028 subject/ENSMUSG00000000028.lst
ENSMUSG00000000037 subject/ENSMUSG00000000037.lst
ENSMUSG00000000049 subject/ENSMUSG00000000049.lst
ENSMUSG00000000056 subject/ENSMUSG00000000056.lst
ENSMUSG00000000058 subject/ENSMUSG00000000058.lst
ENSMUSG00000000078 subject/ENSMUSG00000000078.lst
ENSMUSG00000000085 subject/ENSMUSG00000000085.lst
ENSMUSG00000000088 subject/ENSMUSG00000000088.lst
....
blast_table=Orthologs.list
table_type=family
number_of_threads=16
visualizeAlignment=false
output_path=output
level_2_only=true
alignment_method=gg2
prob_cutoff=0.001
anchor_points=3
gap_size=15
cluster_gap=20
q_value=0.05
I can run the analysis without errors using i-adhore iadhore.ini. However, the resulting alignment.txt file is empty, and the genes.txt file shows column values as 0 for "coordinate, remapped_coordinate, is_tandem, is_tandem_representative, tandem_representative, remapped." Other files also only have column values. Can you help me find the missing point?
Thank you in advance.

[AlbertoBernacchi]

I am having the same issue. Did you manage to solve this?

[kittyBS]

I am having the same issue. Did you manage to solve this?

Hello, I was able to run the analysis without any problems, but since it has been a long time, I do not remember exactly what I did. I only noted that the ortholog file should be tab separated and the .ini file should be space separated. Can you check your files?

[AlbertoBernacchi]

Hi kittyBS,
thank you for the quick response. I'm able to run the analysis without any error but the output files are empty, just as yours were. I checked the files and everything shoud be ok. However, I can't figure how the software would be able to determine gene position just with a list of genes and a table of orthologous genes. Do you remember if you had to add a gff file or something like that to tell i-adhore where the genes should be located in the chromosome?
I'm currently working with mitochondria, so my files look like this:

blast table
gene1+ gene1+
gene2+ gene2+

gene list file.lst
gene1+
gene2+
...

gene list of second organism file.lst
gene1+
gene2+
...

file .ini
genome= ATCC_genes
mitochondrion ATCC_genes.fasta

genome= Pestalotips
mitochondrion2 Pestalotips_genes.fasta

blast_table= ATCC_blast.txt

output_path= output

alignment_method=gg2
gap_size=30
cluster_gap=35
q_value=0.75
prob_cutoff=0.01
anchor_points=3
level_2_only=false
number_of_threads=4

I'm no expert at all, but I think the software is missing some key information to determine synteny (such as the actual locus where the genes are) but I don't know how to submit them...
Thank you again.
-Alberto

[kittyBS]

Since I deleted the directory I was working in, I cannot access the files, but I can share the codes I have with you. Maybe they will be more clear for you. I'm sorry I couldn't be more helpful.
iadhore.txt

[AlbertoBernacchi]

Thank you. As I said I'm very new to bioinformatics, but I will try to get a hang of it. Thank you again for the support.
Best wishes.
-Alberto