Toolbox for generic NGS analyses

Known Issues

Release 0.3.+

  • BWA ALN driving to a ‘EOF error’ on some FASTQ:
  • you are probably using a BWA version between 0.7.2 and 0.7.6. Please use either a 0.6x version or a 0.7.8+ version.
  • Error with options incorporating an equal symbol in their option value.
  • If you have an option such as -l hostname=myNode, it will block if you provide the option basically as -l=hostname=MyNode in the software config file.
  • You can overrride this behaviour using hostanme==MyNode to correct it (see
  • If adaptors are not informed in the software.config for cutadapt (-b options), it will drive to an error in Cutadapt step
  • Cleaner and compressor will drive to an error if a step is too early compressed , i.e. before the pipeline needs it.
  • picardToolsValidateSamFile will always stop the pipeline on an error if the SAM is not perfectly correct. thus, if you want to use this tool, use it as the last one in the pipeline, that will drive whatever to an error.
  • Multiple times repeated software Do not forget to put a space between the software name and the repeated time. Thus samtoolsView 2 functions but not samtoolsView2 !! This convention is requested because of software finishing by a number (e.g. Tophat2) that may be themselves repeated.
  • TOGGLE can generate error Use of uninitialized value $namingConvention in numeric eq (==) at /home/ravel/gitmerge/master/Modules/ line 107 with stacks::processRadtags if you not add option –retain_header on your file_config.txt

*ERROR: toolbox::run : –[E::hts_idx_push] unsorted positions samtools index: “/home/ravel/TOGGLE/DATA-TEST/pairedOneIndividuArcad-noSGE/output/arcad1/5_samToolsView/arcad1.SAMTOOLSVIEW.bam” is corrupted or unsorted