I am trying to use KisSplice 2.6.0 (downloaded 2022-03-25) to detect SNPs in my RNA-seq data and I received the following error:
Traceback (most recent call last):
File "/home/tingyat/.local/kissplice/build/bin/kissplice", line 996, in <module>
main()
File "/home/tingyat/.local/kissplice/build/bin/kissplice", line 913, in main
nb = sort_all_bubbles(internal_bindir, readfiles, workdir, outdir, kval, output_snps, infix_name, not only_graph, options.verbose)
File "/home/tingyat/.local/kissplice/build/bin/kissplice", line 591, in sort_all_bubbles
concatenate_graph_all_log_bcc_to_all_bcc_type0(workdir, kval, output_snps)
File "/home/tingyat/.local/kissplice/build/bin/kissplice", line 464, in concatenate_graph_all_log_bcc_to_all_bcc_type0
destinationSNPS.write(line)
TypeError: a bytes-like object is required, not 'str'
This error only shows up when I included the -s 1 option in my command. Otherwise, KisSplice is able to finish on the default optionhs. I have included the command I used:
~/.local/kissplice/build/bin/kissplice -s 1 -r r1_tyl01.fastq.gz -r r2_tyl03.fastq.gz -r s1_tyl05.fastq.gz -r s2_tyl10.fastq.gz
How can I solve this problem?
Thanks!
1 answer
Dear user,
Thanks for reporting this bug !
It is now fixed. You can get the latest release here: https://gitlab.inria.fr/erable/kissplice/-/releases/2.6.1
If you want to use this version for SNPs, we strongly recommend to use the following parameters:
--mismatches 0 --min_overlap 3
which were the default parameters in versions of KisSplice prior to 2.5.0 and correspond to parameters used for our benchmarks in : https://academic.oup.com/nar/article/44/19/e148/2468394
Best,
Vincent
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