search

DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
124 stars 42 forks source link

bowtie2 is needed but not listed #6

Closed serge2016 closed 7 years ago

serge2016 commented 7 years ago 
root@5f5e7a4b6c25:/outputs/soft/HLA-PRG-LA# ./bin/HLA-PRG-LA --bwa_bin $BWA --samtools_bin /soft/samtools/bin/samtools --BAM /outputs/NA12878.cram --graph ../graphs/PRG_MHC_GRCh38_withIMGT --sampleID NA12878_serge --maxThreads 8 --workingDir ./
....
Directory: tmp/simulatedGraphs/G1
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.02 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.13-r1126
[main] CMD: /soft/bwa.kit/bwa index tmp/simulatedGraphs/G1/referenceGenome/ref.fa
[main] Real time: 0.047 sec; CPU: 0.032 sec
terminate called after throwing an instance of 'std::runtime_error'
  what():  Utilities::findFileFromAlternatives(): No alternative present from C:/Users/AlexanderDilthey/bowtie2-2.2.8, /home/dilthey/bowtie2-2.2.8
Aborted (core dumped)

But bowtie2 is not listed in Prerequisites! And I can't set it's path through an argument! And it is not used from PATH!

serge2016 commented 7 years ago

More over, https://github.com/01org/tbb/releases is also needed! And something like

export LD_LIBRARY_PATH="/soft/bowtie2-2.3.2/tbb2017_20170604oss/lib/intel64/gcc4.7:$LD_LIBRARY_PATH"

is to be done before running HLA-PRG

AlexanderDilthey commented 7 years ago

Neither bowtie2 nor TBB are prerequisites for HLA type inference.