Roadies seems to finish successfully but the final tree is missing

[SimonaSecomandi]

Hi all,

I am running into a issue I don't know how the resolve. The pipeline seems to finish successfully but the final tree is missing.

The only issue I see in the log is this:

...
Finished job 0.
808 of 808 steps (100%) done
Complete log: .snakemake/log/2025-11-05T171852.056824.snakemake.log
cp: cannot stat '{0}/master_gt.nwk': No such file or directory
cp: cannot stat '{0}/master_map.txt': No such file or directory
ASTRAL for PaRalogs and Orthologs III (ASTRAL-Pro3)
...

Those two files are indeed in the correct folder, but the script seems to don't recognize the folder "{0}" defined in .workflow/scripts/converge.py, which should be the output directory I specified in the config file. All the files before this seem to be there.

I can provide the full log via email if needed.

Many thanks!

Simona

[ang037]

Hi,

Thanks for reaching out. As per our README, in default mode, final species tree (in Newick format) for individual iterations will be saved in separate converge_files/iteration_<iteration_number> folders. In your case, it may be saved as iteration_00.nwk inside iteration_00 folder. Could you please check the presence of trees in these folders?

Also, it would be helpful if you could send us the full log file. Thanks.

Regards,
Anshu

[SimonaSecomandi]

Dear Anshu,

thank you for your answer.

In the README and the User guide I read "The output species tree in Newick format will be saved as roadies.nwk in the output_files folder.", which is the one specified with $OUT_DIR, while the iterations are in the $OUT_ALL_DIR.

The files I have in the $OUT_ALL_DIR are:
iteration_00/ iteration_00.nwk iteration_00_stats.nwk iteration_01/ iteration_01.nwk iteration_01_stats.nwk master_gt.nwk master_map.txt time_stamps.csv.

But I don't see the final roadies.nwk tree in the $OUT_DIR folder I guess because of that error in the log I pasted above. I can send you the full log via email.

Please let me know if I need to re run the pipeline or I can use one of the iteration's tree.

Many thanks.

Simona

[ang037]

Your final tree is saved here as iteration_01.nwk

roadies.nwk will be generated only when you run in non-converge mode of operation.

In converge mode (default), since we run multiple iterations, the final tree is saved as tree for the latesr iteration, in your case it's iteration_01.nwk.

Regards,
Anshu

[SimonaSecomandi]

Thank you Anshu, I misunderstood!!

I have a last question. To root my tree, how can I modify the config file?

Many thanks again for the support!

Best,

Simona

[chulbioinfo]

Hi Anshu and Simona,
It would be related to the following script in converge.py

line85 os.system("cp {0}/master_gt.nwk {0}/{1}.gt.nwk".format(out_dir, run))
line86 os.system("cat {0}/{1}/mapping.txt >> {0}/master_map.txt".format(out_dir, run))
line87 os.system("cp {0}/master_map.txt {0}/{1}.map.txt".format(out_dir, run))

I hope it will be helpful.

Best
Chul

[ang037]

ROADIES generates unrooted trees only. You can root the final unrooted tree explicitly by using reroot.py script provided in workflow/scripts/ folder (given a reference rooted species tree as input).

Apologies for the confusion. We will modify our tool and Wiki to clarify this distinction. Thank you for your understanding and for using our tool.