AssertionError: Can only do stranded operations when both PyRanges contain strand info

[leli-li]

I use LAPA on aligned pacbio data from minimap2

I got the following error:

File "/usr/nzx-cluster/apps/lapa/python3.8.11/bin/lapa", line 8, in
sys.exit(cli_lapa())
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/lapa/main.py", line 112, in cli_lapa
lapa(alignment, fasta, annotation, chrom_sizes, output_dir,
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/lapa/lapa.py", line 497, in lapa
_lapa(alignment)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/lapa/lapa.py", line 297, in call
df_cluster = self.annotate_cluster(df_cluster)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/lapa/lapa.py", line 155, in annotate_cluster
df = self.create_genomic_regions().annotate(gr)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/lapa/genomic_regions.py", line 66, in annotate
gr_ann = pr.PyRanges(gr.df, int64=True).join(
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/pyranges/pyranges_main.py", line 2433, in join
dfs = pyrange_apply(_write_both, self, other, **kwargs)
File "/usr/nzx-cluster/apps/lapa/python3.8.11/lib/python3.8/site-packages/pyranges/multithreaded.py", line 207, in pyrange_apply
assert (
AssertionError: Can only do stranded operations when both PyRanges contain strand info

[amdreamer]

Same error on aligned nanopore cDNA data. Do you have solution now?

[amdreamer]

I also tired the test data but still get the error. Here is my script running test data:
lapa
--alignment ./lapa/tests/data/brc1_pb.bam
--fasta ~/Database/genome/human/GRCh38.primary_assembly.genome.chrOnly.fa
--annotation ./lapa/tests/data/brca1.gtf
--chrom_sizes ~/Database/genome/human/GRCh38.primary_assembly.sizes.genome
--output_dir ./LAPA_test
--counting_method tail
--min_tail_len 10

The error:
Traceback (most recent call last):
File "/home/wangmr_cw/install/anaconda3/bin/lapa", line 8, in
sys.exit(cli_lapa())
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/lapa/main.py", line 112, in cli_lapa
lapa(alignment, fasta, annotation, chrom_sizes, output_dir,
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/lapa/lapa.py", line 497, in lapa
_lapa(alignment)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/lapa/lapa.py", line 297, in call
df_cluster = self.annotate_cluster(df_cluster)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/lapa/lapa.py", line 155, in annotate_cluster
df = self.create_genomic_regions().annotate(gr)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/lapa/genomic_regions.py", line 66, in annotate
gr_ann = pr.PyRanges(gr.df, int64=True).join(
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/pyranges/pyranges_main.py", line 2433, in join
dfs = pyrange_apply(_write_both, self, other, **kwargs)
File "/home/wangmr_cw/install/anaconda3/lib/python3.9/site-packages/pyranges/multithreaded.py", line 207, in pyrange_apply
assert (
AssertionError: Can only do stranded operations when both PyRanges contain strand info

[mgandal]

We are getting the same error

[baishengjun]

We are getting the same error. Does anyone solve this problem?
Thanks

[baishengjun]

I resolved my error using pip install pyranges==0.0.111
Hope this can help someone.