Pargenes output :mlsearch_run; bootstraps; support_runs folder output empty.

[anwesha mimi Saha]

Dear Dr. Morel,

Good afternoon,

I am very new to using PARGENES. I tried generating gene trees for my UCE loci obtained from PHYLUCE. My run is completed with no error. However, the respective tree files for each locus are absent in the results.

My commandline after performing a dry run to decide the core

CORES=512

python /home/lpcg/pargenes/pargenes/pargenes.py \
    -a input-alignments-fasta \
    -o input-alignments-fasta-pargenes-bootstraps \
    -d nt \
    -m \
    -c $CORES \
    -b 200

I have attached the entire results for your reference. Please help me resolve the issue. 

Regards,

Ms. Anwesha Saha

PhD Student

Institute of Paleobiology

Polish Academy of Sciences

Warsaw, Poland

-------------------------------------------------------------

Centre for New Technologies (CeNT)

Laboratory for Palaeogenetics and Conservation Genetics.

University of Warsaw

Poland

Warsaw, Poland

---------------------------------------------------------------------

MRes Biodiversity, Evolution & Conservation, UK

--------------------------------------------------------------------------

Former Research Fellow

Ashoka Trust for Research in Ecology & Environment (ATREE)

Bangalore, India

[Benoit Morel]

Hello,

Sorry for the late reply. The command line looks fine. For some reason I can't open the archive. Could you try to compress with another extension (e.g. tar.gz)? Can you also send me the log file separataly, in case it doesn't work again? And if the report.txt file exists, please send it as well.

Best,

Benoit

[Benoit Morel]

Thanks, now I can open the files :-)

I'm not quite sure yet, but I suspect that there is a space in the folder directory (Pilot _pargene):

/mnt/mfs/UCE/UCE_Lagomorph_2022_pilot_phyluce/Cano_all_19_taxa/Pilot _pargene/Cano19_bs200/input-alignments-fasta-pargenes-bootstraps/mlsearch_run/bootstraps/uce-4698_fasta/uce-4698_fasta_bs1

and that this space is causing an error somewhere in the analysis (I think the part after the space is lost somewhere)

Could you try to remove the space and restart the analysis, to see if that works? Let me know if that helps

Best,

Benoit

Le jeu. 24 juil. 2025 à 13:05, anwesha mimi Saha <sahaanwe...@gmail.com> a écrit :

Dear Dr. Morel.

Thank you so much for your reply. I archived the result in "file.tar.gz". I attached the separate log.txt files for each module. There was no separate report.txt, though. However, I found "pilot raxml tree, bootstrap, ...etc." , which I didn't understand. 

Let me know if you need anything else. Please help me resolve this issue. 

Regards,

Anwesha (Mimi)

 file.tar.gz

Ms. Anwesha Saha

PhD Student

 mlsearch_run_logs.txt

 modeltest_logs.txt

 old_parse_logs.txt

 pargenes_logs.txt

 parse_run_logs.txt

 supports_run_logs.txt

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