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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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Fail to sterilize graph (Segmentation fault (core dumped)) #83

Open hqyone opened 1 year ago

hqyone commented 1 year ago

Hi Sir I compiled the HLA-LA on my Ubuntu 20 EC2 with 16 core and 128G ram. It passed the test using the command ../bin/HLA-LA --action testBinary

But got error during prepareGraph PRG_MHC_GRCh38_withIMGT. Following is the error message: [ Thu Jan 5 04:30:34 2023 ] Read graph from ../graphs/PRG_MHC_GRCh38_withIMGT 30200000/30207167[E]

[ Thu Jan 5 04:37:05 2023 ] done [ Thu Jan 5 04:38:04 2023 ] Now serialize (pre-gap-pathindexed) graph to ../graphs/PRG_MHC_GRCh38_withIMGT/serializedGRAPH_preGapPathIndex Segmentation fault (core dumped)

I'm sure I have enough hard driver space and RAM.
bwa = 0.7.17-r1188 samtools=1.13 picard: installed by apt-get install picard-tools

Could you help me to fix the issue?

Thank you so much

AlexanderDilthey commented 1 year ago

Hi @hqyone,

This is very difficult to debug remotely. Could you try running on another machine?

Best wishes

Alex