PaPaRa error "vector::_M_range_check" on protein tree/alignment

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Jeff Mangot

May 31, 2024, 2:18:35 AMMay 31
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Dear all,

After aligning protein sequences of a gene of interest (using mafft) and generating a reference tree (using IQTREE), I wanted to align a set of environmental sequences into the obtained reference tree using PaPaRa. I used the following command line:

papara -a -t ${ref_tree} -s ${ref_alignment} -q ${query_seq} -j 12 -n report

But I obtained the following error message :

terminate called after throwing an instance of 'std::out_of_range'

  what():  vector::_M_range_check

/var/spool/slurm/d/job866081/slurm_script: line 39: 36795 Aborted 

Both reference tree and alignments files are in the write format and try to run this command line on my personal laptop and on the cluster of my institute but got the same error message.

Any idea of the problem here?

Thanks !!

Alexandros Stamatakis

May 31, 2024, 2:29:40 AMMay 31
Which version of Papara are you using?

Could you perhaps send me the input files?

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Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology (Crete lab) (Heidelberg lab)
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