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mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data
http://sourceforge.net/projects/mtoolbox/?source=navbar
GNU General Public License v3.0
90 stars 38 forks source link

./MToolBox.sh: line 346: java: command not found #88

Closed smukh18 closed 4 years ago

smukh18 commented 4 years ago

MToolbox starts running and then gives the following error Outfile saved on /home/smukherjee/Documents/idp/Output/OUT_R6535_C284PACXX_TCCGGAGA_L005_R1_001/OUT.sam. Done.

SAM files post-processing...

SORTING OUT.sam FILES WITH PICARDTOOLS...

./MToolBox.sh: line 346: java: command not found Success.

[E::hts_open_format] fail to open file 'OUT.sam.bam' samtools index: failed to open "OUT.sam.bam": No such file or directory Skip Indel Realigner... cat: OUT.sam.bam: No such file or directory

Please help

clody23 commented 4 years ago

Hi,

you should have java installed to run some of the MToolBox dependancies. Please, make sure you have that installed before running MToolBox.

Best wishes,

Claudia

EricDeveaud commented 3 years ago

sorry I did not think it was so difficult to add few lines to check that java is availble

maybe you would like to copy paste the following.

JAVA=`command -v java`

if [ -z ${JAVA} ]; then
  echo "You need java to run MToolBox"
  exit 1
fi

where ? is up to you. I would personaly set it just after getopt section.

best regards

Eric