binned_bitsets_from_list errors when chromosome size is larger than set MAX (512M) #67

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1. brettChapman commented on Apr 25, 2021

   

   brettChapman

   on Apr 25, 2021

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   Hi, I'm also getting the same error as part of the nf-core/rnaseq pipeline (https://github.com/nf-core/rnaseq). I'm also working with plant genomes.

   inner_distance.py \
         -i Root_1.markdup.sorted.bam \
         -r RGT_Planet.bed \
         -o Root_1 \
          \
         > stdout.txt
     head -n 2 stdout.txt > Root_1.inner_distance_mean.txt
     
     inner_distance.py --version | sed -e "s/inner_distance.py //g" > rseqc.version.txt
   
   Command exit status:
     1
   
   Command output:
     (empty)
   
   Command error:
     WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
     Get exon regions from RGT_Planet.bed ...
     Traceback (most recent call last):
       File "/usr/local/bin/inner_distance.py", line 95, in <module>
         main()
       File "/usr/local/bin/inner_distance.py", line 87, 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 "/usr/local/lib/python3.7/site-packages/qcmodule/SAM.py", line 3582, in mRNA_inner_distance
         exon_bitsets = binned_bitsets_from_list(ref_exons)
       File "/usr/local/lib/python3.7/site-packages/bx/bitset_builders.py", line 143, in binned_bitsets_from_list
         last_bitset.set_range( start, end - start )
       File "lib/bx/bitset.pyx", line 216, in bx.bitset.BinnedBitSet.set_range
       File "lib/bx/bitset.pyx", line 184, in bx.bitset.bb_check_range_count
       File "lib/bx/bitset.pyx", line 180, in bx.bitset.bb_check_index
     IndexError: 537013395 is larger than the size of this BitSet (536870912).
   
2. xvce commented on Apr 28, 2025

   

   xvce

   on Apr 28, 2025

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   Have you resolved this issue? I’m facing it right now. Maybe i can increase the MAX to 1024 * 1024 * 1024, but it requires recompilation.