execution not successful after "graph serialization"

DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data

GNU General Public License v3.0

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execution not successful after "graph serialization" #69

Open miriamsaffern opened 2 years ago

miriamsaffern commented 2 years ago

I installed HLA-LA on my institution's cluster and successfully ran on the provided test file. However, when I try running on my sample (CRAM file) the execution stops after "Graph serialization existing and newer than graph file; read from..." Is there is a reason that it stops here?

miriamsaffern commented 2 years ago

I believe it stopped before the remapping step, since in my temp directory I have the extracted bams but not the remapped bams Is this a problem in that I am not specifying the reference? I don't think that is the case since I didn't get an error that the reference isn't found, and I was able to successfully run with the mini CRAM example file

AlexanderDilthey commented 11 months ago

If it works for the mini CRAM, I would guess it is most likely a memory-related issue.