RseQC geneBody_coverage.py error

[Him26]

Hi, I am trying to run geneBody_coverage.py and I get the following error.
I assume the BinnedBitSet has something to do with transcript legnth so I removed ones that are longer than 500Kb.
But I still get the error.
Can anyone tell me why I am getting the error?
Thank you.

Load BAM file ... Done
Load BAM file ... /opt/gridengine/default/spool/r-slave-1-3/job_scripts/580306: line 9:
python /rseqc/latest/build/scripts-2.7/geneBody_coverage.py --input-f
--out-prefix $3
Get intron regions from /cancer/reference/current/transcriptome/gen.v12.filter
Traceback (most recent call last):
File "/rseqc/latest/build/scripts-2.7/inner_distance.py", line 87, in <module
main()
File "/rseqc/latest/build/scripts-2.7/inner_distance.py", line 79, in main
obj.mRNA_inner_distance(outfile=options.output_prefix,low_bound=options.lower_bound_
s.upper_bound_size,step=options.step_size,refbed=options.ref_gene,sample_size=options.sa
tions.map_qual)
File "/python/python2.7/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x
AM.py", line 3380, in mRNA_inner_distance
exon_bitsets = binned_bitsets_from_list(ref_exons)
File "/python/python2.7/lib/python2.7/site-packages/bx_python-0.7.1-py2.7-lin
set_builders.py", line 143, in binned_bitsets_from_list
last_bitset.set_range( start, end - start )
File "bitset.pyx", line 212, in bx.bitset.BinnedBitSet.set_range (lib/bx/bitset.c:3155
File "bitset.pyx", line 185, in bx.bitset.bb_check_range_count (lib/bx/bitset.c:2669)
IndexError: End (536985336) is larger than the size of this BinnedBitSet (536870912).

[liguow]

There must be very big number(s) in your BED file. If you are working on human/mouse genome, you must have made some mistakes during the preparation of this BED file. However, if you are working on other species which indeed has chromosomes larger than 536870912, please stop using this script.

As you can see from the error message below, bx-python package applied this limitation.

Hi, I am trying to run geneBody_coverage.py and I get the following error.
I assume the BinnedBitSet has something to do with transcript legnth so I removed ones that are longer than 500Kb.
But I still get the error.
Can anyone tell me why I am getting the error?
Thank you.

Load BAM file ... Done
Load BAM file ... /opt/gridengine/default/spool/r-slave-1-3/job_scripts/580306: line 9:
python /rseqc/latest/build/scripts-2.7/geneBody_coverage.py --input-f
--out-prefix $3
Get intron regions from /cancer/reference/current/transcriptome/gen.v12.filter
Traceback (most recent call last):
File "/rseqc/latest/build/scripts-2.7/inner_distance.py", line 87, in <module
main()
File "/rseqc/latest/build/scripts-2.7/inner_distance.py", line 79, in main
obj.mRNA_inner_distance(outfile=options.output_prefix,low_bound=options.lower_bound_
s.upper_bound_size,step=options.step_size,refbed=options.ref_gene,sample_size=options.sa
tions.map_qual)
File "/python/python2.7/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x
AM.py", line 3380, in mRNA_inner_distance
exon_bitsets = binned_bitsets_from_list(ref_exons)
File "/python/python2.7/lib/python2.7/site-packages/bx_python-0.7.1-py2.7-lin
set_builders.py", line 143, in binned_bitsets_from_list
last_bitset.set_range( start, end - start )
File "bitset.pyx", line 212, in bx.bitset.BinnedBitSet.set_range (lib/bx/bitset.c:3155
File "bitset.pyx", line 185, in bx.bitset.bb_check_range_count (lib/bx/bitset.c:2669)
IndexError: End (536985336) is larger than the size of this BinnedBitSet (536870912).