RseQC inner_distance.py error

Question

[him1532]

Hi,

I tried running inner_distance.py script(v2.3.9) on my STAR (v2.1) mapped WTS bam file and I get the following error. Can someone explain why I am getting this error?

Traceback (most recent call last):
  File "/bi_tools/rseqc/latest/build/scripts-2.7/inner_distance.py", line 87, in <module>
    main()
  File "/bi_tools/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_size,up_bound=options.upper_bound_size,step=options.step_size,refbed=options.ref_gene,sample_size=options.sampleSize, q_cut = options.map_qual)
  File "/bi_tools/python/python2.7/lib/python2.7/site-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/qcmodule/SAM.py", line 3380, in mRNA_inner_distance
    exon_bitsets = binned_bitsets_from_list(ref_exons)
  File "/bi_tools/python/python2.7/lib/python2.7/site-packages/bx_python-0.7.1-py2.7-linux-x86_64.egg/bx/bitset_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).

[fabio.liberante]

I am getting the same error. I am sure the solution is simple, but hopefully someone can help!

Answer 1

[fabio.liberante]

I managed to get this working. I think the issue is related to an imperfect BED file. I downloaded a new BED file from UCSC using the GENCODE v23 track with the Basic table. I then used cat hg38_GENCODE_v23_basic | sed "s/^chr//" > hg38_GENCODE_v23_basic.nochr.bed to strip the leading chr marker that isn't used in my STAR-aligned BAM files. Using that new BED file I was able to run inner_distance.py successfully. Good luck!