Error message during SNP analysis with KisSplice

Question

[lm1997]

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!

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

[lm1997]

Thanks! Sorry about that

Answer 1

[vincent.lacroix]

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

[lm1997]

Thanks, Vincent! The snp option -s 1 seems to be working now

[Ram]

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.