Unable to locate pangenome

[kebern]

Hi,

I'm trying to use panorama for pangenome alignment and I got this message:
"FileNotFoundError: Unable to locate one or more pangenome in your file".
But the name and path of pangenome were in the pangenome.tsv files.

Please help me to resolve this.

Thank you.

BK.

[jpjarnoux]

Hi !
Could you share your pangenome.tsv file ?
Also could you use the command with the option --verbose 2 That will give us more info to solve the issue.
Thanks

[kebern]

Hi,
My pangenome.tsv file look like this:
Name Path
pangenomeBcc /ppanggolin_output_DATE2026-02-11_Bcc/pangenomeBcc
pangenomeBpc /ppanggolin_output_DATE2026-02-11_Bpc/pangenomeBpc
pangenomeBpp /ppanggolin_output_DATE2026-02-12_Bpp/pangenomeBpp
pangenomeBsp /ppanggolin_output_DATE2026-02-12_Bsp/pangenomeBsp

I re-run the analyse with --verbose 2 and I got this message:

2026-02-16 12:16:42 align.py:l1063 INFO Loading pangenomes from: pangenomes.tsv
2026-02-16 12:16:42 read_binaries.py:l995 INFO Starting batch pangenome loading from: pangenomes.tsv
2026-02-16 12:16:42 utils.py:l240 ERROR
pangenome_path error
0 Path True
1 /ppanggolin_output_DATE2026-02-11_Bcc/pangenomeBcc True
2 /ppanggolin_output_DATE2026-02-11_Bpc/pangenomeBpc True
3 /ppanggolin_output_DATE2026-02-12_Bpp/pangenomeBpp True
4 /ppanggolin_output_DATE2026-02-12_Bsp/pangenomeBsp True
2026-02-16 12:16:42 read_binaries.py:l1001 ERROR Failed to parse pangenome list file: Unable to locate one or mo>
Traceback (most recent call last):
File "home/bk/.conda/envs/panorama/bin/panorama", line 9, in
sys.exit(main())
^^^^^^
File "/home/bk/.conda/envs/panorama/lib/python3.12/site-packages/panorama/main.py", line 190, in main
align_launcher(args)
File "/home/bk/.conda/envs/panorama/lib/python3.12/site-packages/panorama/alignment/align.py", line 1064,>
pangenomes = load_pangenomes(
^^^^^^^^^^^^^^^^
File "/home/bk/.conda/envs/panorama/lib/python3.12/site-packages/panorama/format/read_binaries.py", line >
pan_to_path = check_tsv_sanity(pangenome_list)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/bk/.conda/envs/panorama/lib/python3.12/site-packages/panorama/utils.py", line 241, in check_t>
raise FileNotFoundError("Unable to locate one or more pangenome in your file.}")
FileNotFoundError: Unable to locate one or more pangenome in your file.}

Thanks you.

[jpjarnoux]

Hi !
You don't need to add a header (name, path), this cause the error.
Also, you should write an absolute path, or a path from where you run the script. This can also be the issue.

Moreover, the error message does not clearly identify which path is missing. This is something we can improve to get the exact path that cause the error.

Please let me know if this solve your issue. In the same time I will create a branch to have a better error management of the error.

Regards

[kebern]

Hi,
Thanks you. I removed "name and path" from a header, wrote absolute path where is my pangenome.h5 file and run my script file from his path but the output still the same ".....FileNotFoundError: Unable to locate one or more pangenome in your file.}".

Regards.

BK.

[jpjarnoux]

I could reproduce partially.

So currently the documentation was wrong. Only absolute path and path from the working directory was working and not relatively to the pangenomes.tsv location. So I add a resolve_path function to solve this issue.

But it does not explain the problem with the absolute path.

Could you please sent me the log with verbose 2 for the absolute path also ?

[kebern]

Hi,

So did I need to re-install the panorama package?
Before re-installed it,

• I re-created new pangenomes.tsv file which was in my working directory, it's look like this:
  pangenome1 ppanggolinBcc/pangenome1.h5
  pangenome2 ppanggolinBpc/pangenome2.h5
  pangenome3 ppanggolinBpp/pangenome3.h5
  pangenome4 ppanggolinBsp/pangenome4.h5

• ppanggolinBcc, ppanggolinBpc, ppanggolinBpp, ppanggolinBsp directory also was in my working directory with my script. I specified each pangenome.h5 file.

• I re-run my panorama script and it's work.

Thanks you.

BK.

[jpjarnoux]

Hi,

So if it works, this way you don't need to reinstall. I will keep the issue open until the fix is added to a new release.

Thanks for your time ! Good catch !

[kebern]

Hi,
Ok.
My pleasure 👍 .

BK.