Wrong version of samtools

root@5f5e7a4b6c25:/outputs/soft/HLA-PRG-LA# samtools --version
samtools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.

./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 ./
....
/home/dilthey/bowtie2-2.2.8/bowtie2 -a -L 25 --omit-sec-seq -x tmp/simulatedGraphs/G1/bowtie2IDX -U tmp/simulatedGraphs/G1/FASTQ/R_1.fq -S tmp/simulatedGraphs/G1/BAM/output_1.bam.sam
1158 reads; of these:
  1158 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    29 (2.50%) aligned exactly 1 time
    1129 (97.50%) aligned >1 times
100.00% overall alignment rate
/soft/samtools/bin/samtools view -bS tmp/simulatedGraphs/G1/BAM/output_1.bam.sam > tmp/simulatedGraphs/G1/BAM/output_1.bam.unsorted
/soft/samtools/bin/samtools sort tmp/simulatedGraphs/G1/BAM/output_1.bam.unsorted tmp/simulatedGraphs/G1/BAM/output_1
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  -@, --threads INT
             Set number of sorting and compression threads [1]
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
terminate called after throwing an instance of 'std::runtime_error'
  what():  Command /soft/samtools/bin/samtools sort tmp/simulatedGraphs/G1/BAM/output_1.bam.unsorted tmp/simulatedGraphs/G1/BAM/output_1 returned code 256
Aborted (core dumped)
DiltheyLab / HLA-LA

Wrong version of samtools #7
