Errors running createFinalHaplotypTable function

[EmilieGllch]

Hello,

I managed to use the package to analyze some markers just fine and I get good results.

However, analyzing some other markers, I get errors running the createFinalHaplotypTable function:
1- "Error in if (snps == "") { : argument is of length zero"
2- "Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord, :
solving row 17: 'allow.nonnarrowing' is FALSE and the supplied start (154) is > refwidth + 1"

(154 is the position of one of the SNP in the list).

I always have results from the firsts steps (the SNPs list, mismatch rate png file etc) ; and these errors are for some samples and not all my dataset.
I would like to know if it means that I cannot have any results for these samples and markers ?

Thank you for your help !

Best regards,

Emilie

[lerch-a]

Hi, This is a bug, which should have been fixed. I will look into the issue on the weekend to figure out why this error still happens. It might be because all reads were filtered out as Chimera, Singletons and Indels. Best, Anita

…

On Nov 5, 2020, at 7:07 AM, EmilieGllch ***@***.***> wrote: Hello, I managed to use the package to analyze some markers just fine and I get good results. However, analyzing some other markers, I get errors running the createFinalHaplotypTable function: 1- "Error in if (snps == "") { : argument is of length zero" 2- "Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 17: 'allow.nonnarrowing' is FALSE and the supplied start (154) is > refwidth + 1" (154 is the position of one of the SNP in the list). I always have results from the firsts steps (the SNPs list, mismatch rate png file etc) ; and these errors are for some samples and not all my dataset. I would like to know if it means that I cannot have any results for these samples and markers ? Thank you for your help ! Best regards, Emilie — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AATLJHD3MIPYTUG74VACCJDSOKIOXANCNFSM4TLI2KUA>.

[EmilieGllch]

Hello,

Thank you for your answer.

I managed to fix the first issue: a nucleotide was missing in the reference sequence I gave in markerFile.txt

However, I'm still struggling with the second issue.. but I understood the error raises from the "createHaplotypOverviewTable" function, command line "snps <- lapply(as.integer(snpSet[,"Pos"]), function(n){ as.character(subseq(sread(sr1), start=n, width = 1)) })"
More precisely, my file ".//frequencyFiles/csp/allSequences_csp_merge.fasta" have some sequences shorter than the reference and since I have a SNP at position 154 and a sequence of 140 nucleotides, this raises an error... I managed to get results by excluding these too short sequences from the fasta file. But I don't understand why I have this problem just for some markers and some patients and not all ? And how can too short sequences be used at this stage of the analysis (final haplotypes) ?

Thanks again !

Best,

Emilie

[lerch-a]

Hi, just noticed that your last message was unanswered.
Did we solve the issue? If not make sure you have the newest version of HaplotypR, as it sounds like a problem (to short sequence) that I solved in the last couple of month.
Thanks