nrun for denovo SV signatures

[AndreVidas]

Dear Palimpsest team.

When reading through your Introduction to Palimpsest, I can see that you recommend nrun = 20 for large data set for SBS/DBS/indel mutational signatures analysis. Is this setting also the recommendation for SV mutational signature analysis? I have used Palimpsest v1.0.0 for SV mutational signature extraction so far and here I have usually used nrun = 100 for large data set (1000 samples), since the recommendation at that time was nrun > 20 for large data set if I remember correctly. Nonetheless, If I try with the newest Palimpsest version and setting nrun = 100, I get an error:

There were 50 or more warnings (use warnings() to see the first 50) Error in [<-.data.frame(*tmp*, , Sig.max.prob.col, value = list(1, : replacement element 38961 is a matrix/data frame of 1 row, need 78479 Calls: signature_origins -> [<- -> [<-.data.frame In addition: Warning message: In [<-.data.frame(*tmp*, , Sig.max.col, value = list("SV_denovo_2.prob", : provided 78479 variables to replace 1 variables Execution halted

Because of this error I'm not able to get the output file generated from the signature_origins() function (containing the probability of each event being due to each process). Furthermore the signature_content_plot.pdf looks pretty weird (attached). Apart from that I get all the other plots and output files correctly generated. Here I get 3 SV signatures in total.

If I set the nrun = 20 for the same data, I instead get 10 signatures, so I'm wondering if nrun = 20 is a good choice. Also, the signature bars in the plot exceeds the figure (attached) and the signature_content_plot.pdf also looks weird as before.

Do you have an idea of what might be causing these problems as well as the best suited nrun? Best regards, André