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PatrickKueck / BaCoCa

BaCoCa (Base Composition Calculator) is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used for a detailed and statistical comprehensive data evaluation. Furthermore, the results can help to identify phylogenetic sequence biases which can lead to incorrect tree reconstructions. The program can handle hundreds of user specified gene and taxon partitions of a single sequence input file in one process run. BaCoCa is a command-line driven program written in PERL and works on WindowsPCs, Macs and Linux operating systems. Therefore, it can be easily integrated into automatic pipeline processes of phylogenomic studies.
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Checkpointing for job management #2

Open ACColin opened 2 years ago

ACColin commented 2 years ago

Hi,

I am running BaCoCa on a HPC cluster and I have seen another issue mentioning the analysis running for multiple days. Does the program support checkpointing the analysis to resume in a subsequent job after reaching the 48h limit? I couldn't find information regarding this in the manual.

Many thanks, Anne-Cecile

edit: the results came back very fast, 48H was way more than enough

PatrickKueck commented 2 years ago

Hallo Anne-Cecile.

 

Sorry for my delayed reply. I was on holiday in the last four weeks.

 

The process time of bacoca depends on the amount of input data. Sometimes it can take more than a day, but usually the overall process time should be shorter. Unfortunately, bacoca is not doing any checkpointings.

 

Best

 

Patrick  

Dr. Patrick Kück Algorithmic Development Leibniz Institute for the Analysis of Biodiversity Change Adenauerallee 160, 53113 Bonn, Germany email: @.*** www.bonn.leibniz-lib.de

   

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Hi,

I am running BaCoCa on a HPC cluster and I have seen another issue mentioning the analysis running for multiple days. Does the program support checkpointing the analysis to resume in a subsequent job after reaching the 48h limit? I couldn't find information regarding this in the manual.

Many thanks, Anne-Cecile

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