Question: RseQC error
gravatar for him1532
3.0 years ago by
him15320 wrote:


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

Traceback (most recent call last):
  File "/bi_tools/rseqc/latest/build/scripts-2.7/", line 87, in <module>
  File "/bi_tools/rseqc/latest/build/scripts-2.7/", 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/", 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/", 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).


myposts • 1.3k views
ADD COMMENTlink modified 2.9 years ago by fabio.liberante10 • written 3.0 years ago by him15320

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

ADD REPLYlink written 2.9 years ago by fabio.liberante10
gravatar for fabio.liberante
2.9 years ago by
fabio.liberante10 wrote:

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 successfully. Good luck!

ADD COMMENTlink written 2.9 years ago by fabio.liberante10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2411 users visited in the last hour