Cannot match signatures after extracting

[eunksung]

Hello,
I was able to generate matrix after I re-install Sigminer using single sample. Also, I was able to extract signatures only when I use the auto extraction without range attribute. However, I keep getting same error when I tried to match signatures and this is the error message: The following components cannot be found in reference!
A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T A[C>T]A A[C>T]C A[C>T]G A[C>T]T A[T>A]A A[T>A]C A[T>A]G A[T>A]T A[T>C]A A[T>C]C A[T>C]G A[T>C]T A[T>G]A A[T>G]C A[T>G]G A[T>G]T C[C>A]A C[C>A]C C[C>A]G C[C>A]T C[C>G]A C[C>G]C C[C>G]G C[C>G]T C[C>T]A C[C>T]C C[C>T]G C[C>T]T C[T>A]A C[T>A]C C[T>A]G C[T>A]T C[T>C]A C[T>C]C C[T>C]G C[T>C]T C[T>G]A C[T>G]C C[T>G]G C[T>G]T G[C>A]A G[C>A]C G[C>A]G G[C>A]T G[C>G]A G[C>G]C G[C>G]G G[C>G]T G[C>T]A G[C>T]C G[C>T]G G[C>T]T G[T>A]A G[T>A]C G[T>A]G G[T>A]T G[T>C]A G[T>C]C G[T>C]G G[T>C]T G[T>G]A G[T>G]C G[T>G]G G[T>G]T T[C>A]A T[C>A]C T[C>A]G T[C>A]T T[C>G]A T[C>G]C T[C>G]G T[C>G]T T[C>T]A T[C>T]C T[C>T]G T[C>T]T T[T>A]A T[T>A]C T[T>A]G T[T>A]T T[T>C]A T[T>C]C T[T>C]G T[T>C]T T[T>G]A T[T>G]C T[T>G]G T[T>G]T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

When I make a table with extracted data, I could see the tally component and this is the result of the head command with the table: TUMOR
T:A[C>A]A 3145
T:A[C>A]C 734
T:A[C>A]G 272
T:A[C>A]T 632
T:A[C>G]A 932
T:A[C>G]C 338

In shell, I also tried to extract the mutation signatures using both maf and sbs as set values for mode. It gave me an error when I used maf as mode: You may choose wrong 'mode' option, this is designed for 'SBS'. However, it generated a SBS_tally.csv file, which is containing information of tally component. When I set sbs as mode, the work has done without an error, but there is no file in the folder.

Because I have total 33 samples, I used maftool to combined them and run both Sigminer and Sigflow, I was fail to extract signatures.

Please, let me know if there are any other information or files that you need to go over the issue.

Thank you.

[ShixiangWang]

Set add_trans_bias = FALSE when you use sig_tally().

[ShixiangWang]

And if you are using get_sig_similarity() to match signatures, and your add_trans_bias = TRUE, you will need to change the option of sig_db = "TSB".

Check https://shixiangwang.github.io/sigminer/reference/get_sig_similarity.html