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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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Assertion `sequencesStream.is_open()' failed. #11

Closed shukwong closed 6 years ago

shukwong commented 6 years ago

Hi,

I am trying to run HLA-PRG-LA with the test.cram and got Assertion `sequencesStream.is_open()' failed. I was wondering if any one else have encountered such an issue and knows how it can be fixed?

Thanks, Wendy

[ Fri Sep 22 15:17:17 2017 ] Remapping done. HLA-PRG-LA: mapper/processBAM.cpp:1173: void mapper::processBAM::initBAM(std::string, bool, bool): Assertion `sequencesStream.is_open()' failed. HLA-PRG-LA execution not successful. Command was ../bin/HLA-PRG-LA --action HLA --maxThreads 4 --sampleID test --outputDirectory /HLA.Typing/HLA_PRG_LA/test/test --PRG_graph_dir /hla-prg-la/src/../graphs/PRG_MHC_GRCh38_withIMGT --FASTQ1 /HLA.Typing/HLA_PRG_LA/test/test/R_1.fastq --FASTQ2 /HLA.Typing/HLA_PRG_LA/test/test/R_2.fastq --bwa_bin /bin/bwa --samtools_bin /SAMtools/1.3/bin/samtools --mapAgainstCompleteGenome 0

shukwong commented 6 years ago

I figured out the issue. I don't have read permission to sequence.txt.