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Hi,

I am new to microhaplot. I was wondering whether the function prepHaplofiles could be used with Nanopore sequencing data?
I have fastq files for a dozen of amplicons; however, as I only sequenced one individual I merged all my fastq files into one only and then mapped that to my reference and used the derived sorted-bam file to do the variantcalling using samtools mpileup | bcftools call.

Thank you very much,
Ettore

There is a problem on one of the plots, and I suspect it is because I installed dplyr 0.8.0 to start testing it.

Right here:

That group_by is grouping on what I will bet are two different factors. (or maybe one factor and a character). At any rate, dplyr 0.8.0 keeps around all the factor levels (include all possible combinations of them) even if they don't occur in the data.

So, Thomas, you need to go through and fix all those for dplyr 0.8.0.

We can talk about it tomorrow.

Not sure it's an issue,

I am trying to use the PrepHaplotFiles() command and when Hapture.pl starts, I get an error
Error in read.table(summary.path, stringsAsFactors = FALSE, sep = "\t") : no lines available in input

I checked all my files (label.txt, sam files, vcf) and I haven't found anything that would be a problem.

Can you tell me the source of the problem with such an error?

From https://cran.r-project.org/web/packages/policies.html

• Packages should not write in the user’s home filespace (including clipboards), nor anywhere else on the file system apart from the R session’s temporary directory (or during installation in the location pointed to by TMPDIR: and such usage should be cleaned up). Installing into the system’s R installation (e.g., scripts to its bin directory) is not allowed.

So, the runHaplot default out.path needs to be set to a temp directory or something. I'm working through it a little bit.

Hi Thomas!
I hope you are doing well. Thanks for creating this great packages. I wanted to alert you to an issue with the SNP report, where some loci get the error invalid 'times' argument. I've checked through the other outputs for these loci and they appear to work fine. Further, "Rejecting" these loci on the locus annotation tab does not filter them out and allow a bulk download of the SNP report. Do you have any suggestions for removing these loci from the SNP report so it can be downloaded, or deciphering why they cause the SNP report portion to break?

Here is a photo of the terminal error

Best,
Liam

Hi,

I'm new to microhaplot and I am getting simple installation problems. I«'ll try to describe this the best I can:

I've followed the instructions in the readme, however, to begin with I don't get 'haPLOType' being created inside Shiny, instead I get another 'microhaplot' directory, which still contains 'server' and 'ui'.
Even so, I proceeded to lunch haPLOType on the example data with 'runShinyHaplot(app.path)' but got:

Loading required package: shiny

Listening on http://127.0.0.1:5314
Error in utils::browseURL(appUrl) :
'browser' must be a non-empty character string

I've checked that the perl version is more recent than required. In any case, I tried running with my data, and I get:

Can't locate Moo.pm in @inc (you may need to install the Moo module) (@inc contains: FatPacked::33105320=HASH(0x1f925a8) /opt/modules/devel/perl/5.18.0/crc/lib/perl5/x86_64-linux /opt/modules/devel/perl/5.18.0/crc/lib/perl5 /opt/modules/devel/perl/5.18.0/crc/lib/5.18.0/x86_64-linux /opt/modules/devel/perl/5.18.0/crc/lib/5.18.0 /opt/modules/devel/perl/5.18.0/crc/lib/site_perl/5.18.0/x86_64-linux /opt/modules/devel/perl/5.18.0/crc/lib/site_perl/5.18.0 /mnt/lfs2/soraia/perl5/lib/perl5 /opt/modules/devel/perl/5.18.0/lib/site_perl/5.18.0/x86_64-linux-thread-multi /opt/modules/devel/perl/5.18.0/lib/site_perl/5.18.0 /opt/modules/devel/perl/5.18.0/lib/5.18.0/x86_64-linux-thread-multi /opt/modules/devel/perl/5.18.0/lib/5.18.0 .) at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 71.
BEGIN failed--compilation aborted at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 71.
Compilation failed in require at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 14859.
BEGIN failed--compilation aborted at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 14859.

If I install Moo, then I get 👍
Can't locate namespace/clean.pm in @inc (you may need to install the namespace::clean module) (@inc contains: FatPacked::27133376=HASH(0x19e05c0) /opt/modules/devel/perl/5.18.0/crc/lib/perl5/x86_64-linux /opt/modules/devel/perl/5.18.0/crc/lib/perl5 /opt/modules/devel/perl/5.18.0/crc/lib/5.18.0/x86_64-linux /opt/modules/devel/perl/5.18.0/crc/lib/5.18.0 /opt/modules/devel/perl/5.18.0/crc/lib/site_perl/5.18.0/x86_64-linux /opt/modules/devel/perl/5.18.0/crc/lib/site_perl/5.18.0 /mnt/lfs2/soraia/perl5/lib/perl5/x86_64-linux-thread-multi /mnt/lfs2/soraia/perl5/lib/perl5 /opt/modules/devel/perl/5.18.0/lib/site_perl/5.18.0/x86_64-linux-thread-multi /opt/modules/devel/perl/5.18.0/lib/site_perl/5.18.0 /opt/modules/devel/perl/5.18.0/lib/5.18.0/x86_64-linux-thread-multi /opt/modules/devel/perl/5.18.0/lib/5.18.0 .) at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 75.
BEGIN failed--compilation aborted at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 75.
Compilation failed in require at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 14859.
BEGIN failed--compilation aborted at /mnt/lfs2/soraia/R/x86_64-pc-linux-gnu-library/3.5/microhaplot/perl/hapture line 14859.
Error in read.table(summary.path, stringsAsFactors = FALSE, sep = "\t") :
no lines available in input

So I'm thinking if you have any idea how to move forward from this, or if I'm missing something earlier on, which makes that these errors keep appearing.

Best,
Soraia

If I do one run call sebastes_testing, and then I do another run called sebastes then it looks like the outputs from the first run will still be around in the directory and then will get bunged into all.summary.

Why not just remove the entire directory intermed and then remake it each time? It seems that would be safer unless there is something that would break.

Greetings! I was wondering how microhaplot handles reads (or read pairs) that do not span all SNPs defined for a marker/amplicon in the VCF file.

In the intermediate files which contain extracted SNP info for each SNP location, it's obvious that "N" would be given to a SNP of it is not covered by the read. However, sometimes, I will also get "X" for some SNP sites, what's the meaning of the "X" here?

A fake example could be:

AATTCCXXTTCCNNN

What do the two "X" in between mean?

In the output pane there should be an option to return information about the actual SNPs that go into the haplotypes. Most notably it would be good to know their positions in the amplicons.

This is coming from some issues Phil Morin is having. He has some reads that have been heavily filtered which creates some Ns at the ends of some haplotypes. He would like to go back and modify the input VCF to remove those SNPs that have a lot of Ns. As it is now, it seems like one has to go back to the original input VCF and then reassociate the info there with the info coming out of microhaplot. It seems like we should be able to make a simple tibble that has that info in it so that we can just download it and get it from a CSV (or inspect it in the output pane).

Cool.

Hello,

I have just tried to re-install microhaplot in my R console (v. 3.6.3) but I keep received the same error message:

"rror: processing vignette 'troubleshoot.Rmd' failed with diagnostics:
E> The 'markdown' package should be installed and declared as a dependency of the 'microhaplot' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'markdown' package. Please see yihui/knitr#1864 for more information."

I am not sure how to fix this. Any idea?

Many thanks,
Ettore