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!

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?

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.

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!

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, 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,

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.

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'

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.

received the above error even when use example data