Open zxl124 opened 4 years ago
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).
I was running RSeQC
inner_distance.py
with a plant species which has large chromosomes (many are > 512Mb). I encountered the following error:After examining biset.py and bitset_builders.py, I think the error was caused by the following hard-coded limit: https://github.com/bxlab/bx-python/blob/1731099ac7e358eb2eced5a02bd4c96ee3c366f0/lib/bx/bitset.pyx#L195
I don't know the reason behind this setting. I am wondering is it possible to increase that to enable dealing with genomes with large chromosomes?