Error loading bedtools/2.22.0

By default, gcc/4.4 is loaded in my cluster environment. This happened when running bedtools:

gcc/4.7.0(5):ERROR:150: Module 'gcc/4.7.0' conflicts with the currently loaded module(s) 'gcc/4.4'
gcc/4.7.0(5):ERROR:102: Tcl command execution failed: conflict gcc/4.4

bedtools/2.22.0(6):ERROR:151: Module 'bedtools/2.22.0' depends on one of the module(s) 'gcc/4.7.0'
bedtools/2.22.0(6):ERROR:102: Tcl command execution failed: prereq gcc/4.7.0

To fix, first module unload gcc/4.4 then module load gcc/4.7.0.

Edited my custom module ‘qsub_sge_file’ function, which I use for all of my commandline bioinformatics pipelines to create a standard bash shell script and qsub submit as job to Sun Grid Engine, to include a line checking if ‘bedtools’ is being loaded:

if any('bedtools' in s for s in module_load):
sge_file.write('module unload gcc/4.4\n')

Then, module load gcc/4.7.0.

for module in module_name_list:
module_load="module load "+module


About Lisa Johnson

PhD candidate at UC Davis in Molecular, Cellular, and Integrative Physiology
This entry was posted in bash, Bioinformatics, Python. Bookmark the permalink.

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