Hello I have a really weird problem
The folder I use to create the ANI map contains those two species

but they are saved as
.

As you can see the last a is missing.

Is there a genome number limit? When I run it with 20-30genomes is fine, but when I input >50 I got error:

Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.10/bin/ANIclustermap", line 8, in <module>
    sys.exit(main())
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/aniclustermap/aniclustermap.py", line 44, in main
    run(
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/aniclustermap/aniclustermap.py", line 93, in run
    fastani_df = parse_fastani_matrix(fastani_matrix_file)
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/aniclustermap/aniclustermap.py", line 231, in parse_fastani_matrix
    with open(matrix_file) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'pl_out2/work/fastani_result.matrix'

Hey, after long time of running the tool without problems, when running ANIclustermap I encountered now the following issue:

# Step1: Run fastani between all-vs-all 13 genomes.
dyld: Library not loaded: @rpath/libopenblasp-r0.3.7.dylib
  Referenced from: /Users/leonidou/opt/anaconda3/envs/ANIclustermap/bin/fastANI
  Reason: image not found
Traceback (most recent call last):
  File "/Users/leonidou/opt/anaconda3/envs/ANIclustermap/bin/ANIclustermap", line 10, in <module>
    sys.exit(main())
  File "/Users/leonidou/opt/anaconda3/envs/ANIclustermap/lib/python3.8/site-packages/aniclustermap/aniclustermap.py", line 29, in main
    run(**args.__dict__)
  File "/Users/leonidou/opt/anaconda3/envs/ANIclustermap/lib/python3.8/site-packages/aniclustermap/aniclustermap.py", line 75, in run
    ani_df = parse_ani_matrix(ani_matrix_file)
  File "/Users/leonidou/opt/anaconda3/envs/ANIclustermap/lib/python3.8/site-packages/aniclustermap/aniclustermap.py", line 229, in parse_ani_matrix
    with open(matrix_file) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'ANIclustermap_Results/work/fastani_result.matrix'

It must be something with the dyld library that I was not able to fix.
The tool worked so far perfectly for me, and suddenly I get this error..Thanks in advance!

Hey, when running ANIclustermap I encountered the following issues:

# Step1: Run fastANI between all-vs-all 7 genomes.
/bin/sh: fastANI: command not found
Traceback (most recent call last):
  File "/Users/leonidou/opt/anaconda3/bin/ANIclustermap", line 8, in <module>
    sys.exit(main())
  File "/Users/leonidou/opt/anaconda3/lib/python3.8/site-packages/aniclustermap/aniclustermap.py", line 44, in main
    run(
  File "/Users/leonidou/opt/anaconda3/lib/python3.8/site-packages/aniclustermap/aniclustermap.py", line 93, in run
    fastani_df = parse_fastani_matrix(fastani_matrix_file)
  File "/Users/leonidou/opt/anaconda3/lib/python3.8/site-packages/aniclustermap/aniclustermap.py", line 231, in parse_fastani_matrix
    with open(matrix_file) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'Results/work/fastani_result.matrix'

Could you please help me how to resolve the issue? Many thanks in advance!

Hi,
I am trying to run this tool and encountered this error

Step1: Run fastani between all-vs-all 41 genomes.

/bin/sh: fastANI: command not found
Traceback (most recent call last):
File "/Users/emmannaemeka/mambaforge/bin/ANIclustermap", line 8, in
sys.exit(main())
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/aniclustermap/aniclustermap.py", line 29, in main
run(**args.dict)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/aniclustermap/aniclustermap.py", line 75, in run
ani_df = parse_ani_matrix(ani_matrix_file)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/aniclustermap/aniclustermap.py", line 229, in parse_ani_matrix
with open(matrix_file) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'anicluster_map/work/fastani_result.matrix'

Hey, I came accross you piece when looking for a way to visulize the fastANI output. So I was wondering if it is possible to input an existing fastANI output into your ANIclustermap.

All the best,
Lisa

Hi,

Is it possible to have a special range color for taxonomist user or the possibility to define (by a configuration file) a range by color ?

For the taxonomist user, they like to have a color range of 100% ANI, 99%-95%, 94%-83%, 82%-70% and 70%-0%.

Thanks for your work.

Have a good day.

Thank you for providing this incredible tool!
However, I’ve encountered an issue with the output and its annotations.
According to the tutorial, the expected output should look like this:

However, when I reproduced the same dataset and used the same code, the actual output I obtained was as follows:

Code:
ANIclustermap -i normal_dataset/normal_dataset/ -o ANIclustermap_result --fig_width 20 --fig_height 15 --annotation

Thank you for your help!

Hi,

Second issue to enhance this tools =)

Most People use differents tools for ANI score like OrthoANI or want to use AAI score or mash distance values, all theses tools produce a similarity matrix file.

Is it possible to bypass the FastANI step in your tool by directly passing the similarity matrix (tsv/csv format) ?

Thanks in advance for your work.

Have a good day.

received the above error even when use example data

Dear all,
I have downloaded some strain assemblies (looking like files GCF_000014505.1_ASM1450v1_genomic.fna)
In the folder I have put my strain assembly fna file, but whatever name I give to my file it is not present in the png, and I see that workflow loads all files but mine (and I checked the fasta is fine)? Can you help?