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MPBoot problem #250

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IanMarquezIDIBAPS opened this issue Jul 28, 2023 · 0 comments
Open

MPBoot problem #250

IanMarquezIDIBAPS opened this issue Jul 28, 2023 · 0 comments

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@IanMarquezIDIBAPS
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Hi everyone,
I've been trying to run MPBoot for a fasta file containing 30 sequences of 351 nucleotides each. The structure is something like:

>sample_sc1
ACGTACGTACGT...
>sample_sc2
ACGTACGTACGT...

The command used for running MPBoot has been:
mpboot -s /path/sample.fasta -bb 1000

We have some experience running MPBoot with binary matrices, but we also thought that it worked for DNA sequences. When running this command we obtain the following error:

Time for parsimony tree construction: 0.004 seconds
Parsimony score: 96
Reordering patterns in alignment by decreasing order of pattern parsimony... 0.000 seconds

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.003 seconds
Generating 1000 samples for bootstrap approximation...

NOTE: 0.335 MB RAM is required!
Current best tree score: 95

Generating 99 parsimony trees... (0 duplicated parsimony trees)
CPU time: 0
Finish initializing candidate tree set. Number of distinct locally optimal trees: 100
Current best score: 93 / CPU time: 0

Time: 0h:0m:0s

*** MPBoot CRASHES WITH SIGNAL ABORTED
*** For bug report please send developers:
*** Log file: /home/ubuntu/Desktop/StarLife_server/projects/cli79/scMCL/GEX/5_BCR_analysis//Phylogenies/05-229/05-229.fasta.log
*** Alignment files (if possible)

Then, the output directory contains the .log, .parstree and .treefile outputs, but not the consensus tree. Could you please tell me if there could be any problem with the input or the command writen?

Thank you so much kindly,

Ian

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