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Error with the sample data #4

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atlasbioinfo opened this issue Mar 17, 2022 · 0 comments
Open

Error with the sample data #4

atlasbioinfo opened this issue Mar 17, 2022 · 0 comments

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@atlasbioinfo
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Hi there,
Thank you for providing this software.
However, while running the sample data, I encountered an issue that made the interrupt.

Traceback (most recent call last):
File "/home/atlas/anaconda3/envs/RG4SEEK/bin/rG4-seeker", line 8, in
sys.exit(main())
File "/home/atlas/anaconda3/envs/RG4SEEK/lib/python3.7/site-packages/rg4seeker/main.py", line 223, in main
main_driver(sys.argv[1])
File "/home/atlas/anaconda3/envs/RG4SEEK/lib/python3.7/site-packages/rg4seeker/main.py", line 216, in main_driver
whitelist_beds, rg4_motif_beds, annotation_names, annotation_gffs)
File "/home/atlas/anaconda3/envs/RG4SEEK/lib/python3.7/site-packages/rg4seeker/apriori_rts_analysis.py", line 930, in main
single_cond_rts_arrays, transcriptome_dict)
File "/home/atlas/anaconda3/envs/RG4SEEK/lib/python3.7/site-packages/rg4seeker/apriori_rts_analysis.py", line 809, in rts_analyze
HTSeq.GenomicPosition(rts_iv.chrom, i, rts_iv.strand)]
File "src/HTSeq/_HTSeq.pyx", line 696, in HTSeq._HTSeq.GenomicArray.getitem
File "src/HTSeq/_HTSeq.pyx", line 463, in HTSeq._HTSeq.ChromVector.getitem
IndexError

In addition, I feel that this software is very strict about the format of the gff annotation file. I get stuck at the "whitelist" generation step when I switch to the Arabidopsis file.
Anyway, the issue of sample data is more important.
Many thanks~

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