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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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Segmentation fault #116

Closed spencer411 closed 3 years ago

spencer411 commented 3 years ago

I am trying to use this program, but I get a segmentation fault error. I am running it as follows and get the corresponding error:

(clonalframeml) -bash-4.2$ ClonalFrameML aureus_tree.tre core_alignment.xmfa clonal_out -xmfa_file true

ClonalFrameML v1.12 xmfa_file = true Finished reading in control file.

/tmp/slurmd/job2421871/slurm_script: line 14: 42011 Segmentation fault ClonalFrameML aureus_tree.tre core_alignment.xmfa clonal_out -xmfa_file true

Note that my .xmfa file is pretty large (125MB). I have tried running it on a smaller .fa file to test with no problem. Any help is appreciated.

xavierdidelot commented 3 years ago

I think your previous problem was because you were not using the argument "-xmfa_file true" The segmentation fault is harder to diagnose. 125MB should be no problem at all. Could you try to run on just the first two loci of your xmfa file, so truncating this file after the second "=" symbol?

spencer411 commented 3 years ago

I created a .fa file instead and it seems to be working fine now. It may have been a problem with some of the characters which I have since replaced with "N". Seems to be running well. Thanks so much for the speedy reply!