There is only one bedtools in the path, the one installed by bcbio, so I was wondering what might be the source of error. Please install a more recent version of BEDTools and re-import to use this method.

NotImplementedError: 'subtractBed' does not appear to be installed or on the path, so this method is disabled. If len(ref_regions.subtract(nblock_regions, nonamecheck=True)) > 0:įile '/pico/home/userexternal/esebesty/work/bcbio/data/anaconda/lib/python2.7/site-packages/pybedtools/bedtool.py', line 773, in decoratedįile '/pico/home/userexternal/esebesty/work/bcbio/data/anaconda/lib/python2.7/site-packages/pybedtools/bedtool.py', line 203, in not_implemented_func Return ipython.zip_args(apply(sample.postprocess_alignment, *args))įile '/pico/home/userexternal/esebesty/work/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py', line 184, in postprocess_alignmentĬallable.block_regions(bam_file_ready, ref_file, data)įile '/pico/home/userexternal/esebesty/work/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/bam/callable.py', line 338, in block_regions

When testing the cineca-fix branch of ipython cluster helper I get the following error, after installing a brand new stable version of bcbio: node019: bedtools groupby coverage: Y : LUAD_7763_01A_TP-sort.bamįile '/pico/home/userexternal/esebesty/work/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py', line 50, in _setup_loggingįile '/pico/home/userexternal/esebesty/work/bcbio/data/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py', line 187, in postprocess_alignment

Install pybedtools cygwin anaconda