Hello everyone.
I've got a problem installing HaplotypR, would you mind giving me a clue or guiding me during the process?
thank you so much!
Rotha

Hi Anita,

I hope you are doing well. I am trying to figure out how HaplotypR works in regards of DNA read reconstruction. Because I am working with markers which length is about 800 bp, I was wondering if there is a step where HaplotypR reconstructs my reads to the original size and gets the haplotypes out of each one of them. Because I used Nextera in my experiments, there was some random shearing of my fragments, and I get reads of 250 bp of size. Basically my question is, will HaplotypR do haplotyping based on my 250 bp reads alone? Or will it reconstruct my reads to the original haplotype and then do haplotype calling? I am afraid I could be getting something like this:

where I get the variation only in one part of my marker.

Thanks in advance,

Daniel

I found these bugs, misspellings, or replacement during the script:

procReads <- mergeAmpliconReads(as.character(dePlexMarker$FileR1), as.character(dePlexMarker$FileR2), outProcFiles)
procReads <- cbind(dePlexMarker[,c("SampleID", "SampleName","BarcodePair", "MarkerID")], procReadsMerge)

I think it should be as this, instead:

procReadsMerge <- mergeAmpliconReads(as.character(dePlexMarker$FileR1), as.character(dePlexMarker$FileR2), outProcFiles)
procReads <- cbind(dePlexMarker[,c("SampleID", "SampleName","BarcodePair", "MarkerID")], procReadsMerge)

That would be nice and helpful if for all the script you reformat the code Ctrl+Shift+A/ Cmd+Shift+A

I have a question, for “Calculate mismatch rate and call SNPs” and “Call Haplotypes” what should be my outputDir, I having bugs in both calls

Thank you in advance,

Hi,
I am using HaplotypR and now I can get, for each of the samples, the reads associated with each of the haplotypes. Could it be possible to get the sequence of these haplotypes?
Bests,
Carlos Ruiz

Hi,
I was able to run through the tutorial on the github main page but I was wondering what files from the final directories we should use for further downstream analysis?

Thanks!

• Nick

Hi! I am trying HaplotypR with the example data and I have not been able to run the last step. When I run:

finalTab <- createFinalHaplotypTable(outputDir=outputDir, sampleTable=procReads, 
                                     snpList=snpLst, postfix=postfix, 
                                     minHaplotypCoverage=minCov, minReplicate=minOccHap, 
                                     detectability=detectionLimit, minSampleCoverage=minCovSample)

The function runs and process the samples. However, it stops with the following error:

Error: 'lengths' is not an exported object from 'namespace:S4Vectors'

I have noticed that the error is in the function createHaplotypOverviewTable, which explicitly calls to S4Vectors::lengths (line 150 of filterHaplotype.R). Have you experienced any similar problem? I send you my sessionInfo() at the end, in case it is a version issue. I have not copied the full traceback as it is very long.

I have also had another problem running this function. The first time I run the function, I got a very premature error:

Error in if (getOption("HaplotypR.devel")) write.table(tab, file = file.path(outputDir,  :
  argumento tiene longitud cero

I have solved this problem by manually setting this option:

options(HaplotypR.devel = FALSE)

Would it be possible to also solve this issue.
Bests,
Carlos Ruiz

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /home/isglobal.lan/cruiz/lib64/R/lib/libRblas.so
LAPACK: /home/isglobal.lan/cruiz/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] Rvsearch_0.99.1             Rswarm_0.99.1
 [3] ShortRead_1.42.0            GenomicAlignments_1.20.1
 [5] SummarizedExperiment_1.14.0 DelayedArray_0.10.0
 [7] matrixStats_0.54.0          Biobase_2.44.0
 [9] Rsamtools_2.0.0             GenomicRanges_1.36.0
[11] GenomeInfoDb_1.20.0         BiocParallel_1.18.0
[13] Biostrings_2.52.0           XVector_0.24.0
[15] IRanges_2.18.1              S4Vectors_0.22.0
[17] BiocGenerics_0.30.0         HaplotypR_0.3

loaded via a namespace (and not attached):
 [1] zlibbioc_1.30.0        lattice_0.20-38        hwriter_1.3.2
 [4] tools_3.6.0            grid_3.6.0             latticeExtra_0.6-28
 [7] Matrix_1.2-17          GenomeInfoDbData_1.2.1 RColorBrewer_1.1-2
[10] bitops_1.0-6           RCurl_1.95-4.12        compiler_3.6.0

Hi! I'm having a problem while running my gene markers. I've uploaded my files in a similar way as you have it in your test folder, however when I encounter the trimming process I get null values when trying to save as a fasta file:

``

numNtF <- 190
numNtR <- 120
postfix <- sprintf("bind%.0f%.0f", numNtF, numNtR)

Adjust reference to trim options and save as fasta file

refSeq <- as.character(markerTab$ReferenceSequence)
refSeq <- DNAStringSet(paste(substr(refSeq, 1,numNtF), substr(refSeq, nchar(refSeq)+1-numNtR, nchar(refSeq)), sep=""))
names(refSeq) <- markerTab$MarkerID
lapply(seq_along(refSeq), function(i){

• writeFasta(refSeq[i], file.path(outputDir, paste(names(refSeq)[i], postfix, ".fasta", sep="")))
• })
  [[1]]
  NULL

[[2]]
NULL
``

This ultimately leads to the following message:
Processing file NA and NA1 Error in open.connection(con, "rb") : cannot open the connection In addition: Warning message: In open.connection(con, "rb") : cannot open file 'NA': No such file or directory

Do you know what could it be?

Thanks in advance

Dear Lerch,

I am facing problems to install Rswarm_0.99.1-win_R-v4.1 and Rvsearch_0.99.1-win_R-v4.1 on Windows 10, R version 4.1.0, as you can see below:

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0 rstudioapi_0.15.0

I have also Rtools installed!

I downloaded the binary zip files to a local folder and executed the install.packages() command as described in your instructions, however, I always get the following error message:

setwd("~/NGS/R_packages_haplotypes")
install.packages("Rswarm_0.99.1-win_R-v4.1.zip", repos = NULL)
Installing package into ‘C:/Users/ITM/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open compressed file 'Rswarm_0.99.1-win_R-v4.1/DESCRIPTION', probable reason 'No such file or directory'
Error in install.packages : cannot open the connection

Could you help me to solve this problem?

Thanks in advance.

Douglas

hi,
i'm countering issue installing Rswarm (and Rvsearch) :

path <- file.path(tempfile(pattern="Rswarm-"), "Rswarm")
dir.create(path, recursive=TRUE)
repo <- clone("https://github.com/lerch-a/Rswarm.git", path)
cloning into 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc/Rswarm'...
Receiving objects: 1% (1/51), 21 kb
Receiving objects: 11% (6/51), 21 kb
Receiving objects: 21% (11/51), 21 kb
Receiving objects: 31% (16/51), 21 kb
Receiving objects: 41% (21/51), 21 kb
Receiving objects: 52% (27/51), 21 kb
Receiving objects: 62% (32/51), 21 kb
Receiving objects: 72% (37/51), 21 kb
Receiving objects: 82% (42/51), 21 kb
Receiving objects: 92% (47/51), 21 kb
Receiving objects: 100% (51/51), 21 kb, done.
clone("https://github.com/torognes/swarm.git", file.path(path, "src", "swarm"))
cloning into 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc/Rswarm/src/swarm'...
Receiving objects: 1% (43/4233), 63 kb
Receiving objects: 11% (466/4233), 127 kb
Receiving objects: 21% (889/4233), 407 kb
Receiving objects: 31% (1313/4233), 463 kb
Receiving objects: 41% (1736/4233), 575 kb
Receiving objects: 51% (2159/4233), 688 kb
Receiving objects: 61% (2583/4233), 856 kb
Receiving objects: 71% (3006/4233), 1640 kb
Receiving objects: 81% (3429/4233), 2649 kb
Receiving objects: 91% (3853/4233), 3545 kb
Receiving objects: 100% (4233/4233), 3666 kb, done.
Local: master C:/Users/abate/AppData/Local/Temp/RtmpU561F2/Rswarm-25acf6e2dcc/Rswarm/src/swarm
Remote: master @ origin (https://github.com/torognes/swarm.git)
Head: [4bf8bfc] 2021-04-26: revert static_cast removal (compilation errors with GCC 4.8 and 4.9)
install(path)
checking for file 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc\Rswarm/DESCRIPTION' ... checking for file 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc\Rswarm/DESCRIPTION' ... √ checking for file 'C:\Users\abate\AppData\Local\Temp\RtmpU561F2\Rswarm-25acf6e2dcc\Rswarm/DESCRIPTION'
- preparing 'Rswarm':
checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... √ checking DESCRIPTION meta-information

• cleaning src
  - checking for LF line-endings in source and make files and shell scripts
  - checking for empty or unneeded directories
  - building 'Rswarm_0.99.1.tar.gz'

Running "C:/PROGRA1/R/R-401.2/bin/x64/Rcmd.exe" INSTALL
"C:\Users\abate\AppData\Local\Temp\RtmpU561F2/Rswarm_0.99.1.tar.gz"
--install-tests

• installing to library 'C:/Users/abate/Documents/R/win-library/4.0' * installing source package 'Rswarm' ... ** using staged installation ** libs aucune DLL n'a pas été créé ERROR: compilation failed for package 'Rswarm' * removing 'C:/Users/abate/Documents/R/win-library/4.0/Rswarm' Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
  System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
  Type .Last.error.trace to see where the error occurred

.Last.error.trace
Stack trace:

1. devtools:::install(path)
2. pkgbuild::with_build_tools(required = FALSE, callr::rcmd("INSTALL", ...
3. withr::with_path(rtools_path(), code)
4. base:::force(code)
5. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
6. callr:::run_r(options)
7. base:::with(options, with_envvar(env, do.call(processx::run, ...
8. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
9. base:::eval(substitute(expr), data, enclos = parent.frame())
10. base:::eval(substitute(expr), data, enclos = parent.frame())
11. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmd ...
12. base:::force(code)
13. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
14. (function (command = NULL, args = character(), error_on_status = TRUE, ...
15. throw(new_process_error(res, call = sys.call(), echo = echo, ...
    x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed

Do you know how can I resolve it please.
I'm on W10.

Thanks

Hello! Thank you for all your work!
I have a question about one the HaplotypR functions.

I am working on MiSeq data with the HaplotypR package. I have 35 samples with five P. falciparum markers: ama1-d3, cpmp, csp, cpp and msp7.
I could proceed with the following steps using an R code I received from the WEHI in December 2019:

• demultiplexing by sample
• demultiplexing by marker
• read quality per marker

I am then trying to merge paired ends but I am encountering different issues depending on the syntax I am trying:

Syntax 1:

>   merged_reads <- 
+     marker_deplex %>%
+     select(SampleID, SampleName, MarkerID) %>%
+     bind_cols(mergeAmpliconReads(marker_deplex$FileR1, 
+                                                         marker_deplex$FileR2,
+                                                         outputDir = 'merge_reads'))
Processing file 3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_F.fastq.gz and 3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_R.fastq.gz ...1
Warning in if (method == "vsearch") { :
  the condition has length > 1 and only the first element will be used
Warning in system(call, intern = TRUE) :
  running command '"C:/Users/apepey/Documents/R/R-4.1.2/library/Rvsearch/vsearch" --fastq_mergepairs "marker_deplex/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_F.fastq.gz" --reverse "marker_deplex/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_R.fastq.gz" --fastqout "merge_reads/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_merge.fastq.gz" --fastq_truncqual 1 --fastq_maxns 0 --fastq_allowmergestagger' had status 1
Error: Input/Output
  no input files found
  dirPath: merge_reads/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_merge.fastq.gz
  pattern: character(0)

Syntax 2:

>   merged_reads <- 
+     marker_deplex %>%
+     mergeAmpliconReads(fastqFileR1 = marker_deplex$FileR1, 
+                                         fastqFileR2 = marker_deplex$FileR2,
+                                         outputDir = 'merge_reads')
Processing file 3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_F.fastq.gz and 3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_R.fastq.gz ...1
Warning in if (method == "vsearch") { :
  the condition has length > 1 and only the first element will be used
Warning in if (method == "NGmerge") { :
  the condition has length > 1 and only the first element will be used
Error in FUN(X[[i]], ...) : 
  Merge c("3D7-A", "3D7-A", "3D7-A", "3D7-A", "3D7-A", "3D7-B", "3D7-B", "3D7-B", "3D7-B", "3D7-B", "M0-176", "M0-176", "M0-176", "M0-176", "M0-176", "M0-316", "M0-316", "M0-316", "M0-316", "M0-316", "M0-441", "M0-441", "M0-441", "M0-441", "M0-441", "M0-445", "M0-445", "M0-445", "M0-445", "M0-445", "M0-5", "M0-5", "M0-5", "M0-5", "M0-5", "M0-561", "M0-561", "M0-561", "M0-561", "M0-561", "M0-562", "M0-562", "M0-562", "M0-562", "M0-562", "M0-687", "M0-687", "M0-687", "M0-687", "M0-687", "M0-801", "M0-801", 
"M0-801", "M0-801", "M0-801", "M0-96", "M0-96", "M0-96", "M0-96", "M0-96", "M1-316", "M1-316", "M1-316", "M1-316", "M1-316", "M1-561", "M1-561", "M1-561", "M1-561", "M1-561", "M1-687", "M1-687", "M1-687", "M1-687", "M1-687", "M1-801", "M1-801", "M1-801", "M1-801", "M1-801", "M1-831", "M1-831", "M1-831", "M1-831", "M1-831", "M11-441", "M11-441", "M11-441", "M11-441", "M11-441", "M11-792", "M11-792", "M11-792", "M11-792", "M11-792", "M2-445", "M2-445", "M2-445", "M2-445", "M2-445

Syntax 3:

>   merged_reads <-
+     marker_deplex %>%
+     select(SampleID, SampleName, MarkerID) %>% 
+     bind_cols(mergeAmpliconReads(fastqFileR1 = as.character(marker_deplex$FileR1), 
+                                                         fastqFileR2 = as.character(marker_deplex$FileR2),
+                                                         outputDir = './merge_reads'))
Processing file 3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_F.fastq.gz and 3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_R.fastq.gz ...1
Warning in if (method == "vsearch") { :
  the condition has length > 1 and only the first element will be used
Warning in system(call, intern = TRUE) :
  running command '"C:/Users/apepey/Documents/R/R-4.1.2/library/Rvsearch/vsearch" --fastq_mergepairs "marker_deplex/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_F.fastq.gz" --reverse "marker_deplex/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_R.fastq.gz" --fastqout "./merge_reads/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_merge.fastq.gz" --fastq_truncqual 1 --fastq_maxns 0 --fastq_allowmergestagger' had status 1
Error: Input/Output
  no input files found
  dirPath: ./merge_reads/3D7-A_BC_GTAAGGAG-CGTACTAG_cpmp_merge.fastq.gz
  pattern: character(0)

Syntax 4:

>   merged_reads <-
+     marker_deplex %>%
+     mergeAmpliconReads(as.character(marker_deplex$FileR1), 
+                                         as.character(marker_deplex$FileR2),
+                                         outputDir = './merge_reads')
Error in mergeAmpliconReads(., as.character(marker_deplex$FileR1), as.character(marker_deplex$FileR2),  : 
  Vector length of fastqFileR1 and fastqFileR2 not identical

What could I try to merge paired ends?
Any help is appreciated, thank you.
My marker_table is available here: https://gist.github.com/APepey/054e40b9a10f4b25987dc73b3421e2f5

Here is my session info:

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 
 
locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Rvsearch_0.99.1             cowplot_1.1.1               dada2_1.21.0                Rcpp_1.0.7                  HaplotypR_0.3.3            
 [6] devtools_2.4.3              usethis_2.1.5               ShortRead_1.52.0            GenomicAlignments_1.30.0    SummarizedExperiment_1.24.0
[11] Biobase_2.54.0              MatrixGenerics_1.6.0        matrixStats_0.61.0          Rsamtools_2.10.0            GenomicRanges_1.46.1       
[16] Biostrings_2.62.0           GenomeInfoDb_1.30.0         XVector_0.34.0              IRanges_2.28.0              S4Vectors_0.32.3           
[21] BiocParallel_1.28.3         BiocGenerics_0.40.0         pheatmap_1.0.12             forcats_0.5.1               stringr_1.4.0              
[26] dplyr_1.0.7                 purrr_0.3.4                 tidyr_1.1.4                 tibble_3.1.6                ggplot2_3.3.5              
[31] tidyverse_1.3.1             readr_2.1.1                

loaded via a namespace (and not attached):
 [1] colorspace_2.0-2       hwriter_1.3.2          ellipsis_0.3.2         rprojroot_2.0.2        fs_1.5.2               rstudioapi_0.13       
 [7] farver_2.1.0           remotes_2.4.2          bit64_4.0.5            fansi_0.5.0            lubridate_1.8.0        xml2_1.3.3            
[13] cachem_1.0.6           knitr_1.37             pkgload_1.2.4          jsonlite_1.7.3         broom_0.7.11           dbplyr_2.1.1          
[19] png_0.1-7              compiler_4.1.2         httr_1.4.2             backports_1.4.1        assertthat_0.2.1       Matrix_1.4-0          
[25] fastmap_1.1.0          cli_3.1.0              htmltools_0.5.2        prettyunits_1.1.1      tools_4.1.2            gtable_0.3.0          
[31] glue_1.6.0             GenomeInfoDbData_1.2.7 reshape2_1.4.4         cellranger_1.1.0       vctrs_0.3.8            xfun_0.29             
[37] ps_1.6.0               testthat_3.1.1         rvest_1.0.2            lifecycle_1.0.1        zlibbioc_1.40.0        scales_1.1.1          
[43] vroom_1.5.7            hms_1.1.1              parallel_4.1.2         RColorBrewer_1.1-2     yaml_2.2.1             memoise_2.0.1         
[49] latticeExtra_0.6-29    stringi_1.7.6          desc_1.4.0             pkgbuild_1.3.1         rlang_0.4.12           pkgconfig_2.0.3       
[55] bitops_1.0-7           evaluate_0.14          lattice_0.20-45        labeling_0.4.2         bit_4.0.4              tidyselect_1.1.1      
[61] processx_3.5.2         plyr_1.8.6             magrittr_2.0.1         R6_2.5.1               snow_0.4-4             generics_0.1.1        
[67] DelayedArray_0.20.0    DBI_1.1.2              pillar_1.6.4           haven_2.4.3            withr_2.4.3            RCurl_1.98-1.5        
[73] modelr_0.1.8           crayon_1.4.2           utf8_1.2.2             tzdb_0.2.0             rmarkdown_2.11         jpeg_0.1-9            
[79] grid_4.1.2             readxl_1.3.1           callr_3.7.0            reprex_2.0.1           digest_0.6.29          RcppParallel_5.1.5    
[85] munsell_0.5.0          sessioninfo_1.2.2  

Thank you again!

Hi! I was wondering if the reference column that you have in your marker file refers to an example of a read that has the primers in it? Or what does this reference stand for? Can I upload a file with only the forward and reverse primers without the reference?

Thanks!

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

Hello,

I am trying to run the example data and I keep receiving an error during the "Run demultiplex by marker and truncate primer sequence" step.  

dePlexMarker <- demultiplexByMarker(dePlexSample, markerTab, outDeplexMarker)
Processing marker csp
Processing file R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz and R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz
Processing file R-500_Rep2_BC_Fwd_02-Rev_10_R1.fastq.gz and R-500_Rep2_BC_Fwd_02-Rev_10_R2.fastq.gz
Processing file R-1000_Rep2_BC_Fwd_03-Rev_10_R1.fastq.gz and R-1000_Rep2_BC_Fwd_03-Rev_10_R2.fastq.gz
Processing file R-1500_Rep2_BC_Fwd_04-Rev_10_R1.fastq.gz and R-1500_Rep2_BC_Fwd_04-Rev_10_R2.fastq.gz
Processing file R-3000_Rep2_BC_Fwd_05-Rev_10_R1.fastq.gz and R-3000_Rep2_BC_Fwd_05-Rev_10_R2.fastq.gz
Processing file R-1_Rep2_BC_Fwd_06-Rev_09_R1.fastq.gz and R-1_Rep2_BC_Fwd_06-Rev_09_R2.fastq.gz
Processing file R-10_Rep2_BC_Fwd_07-Rev_09_R1.fastq.gz and R-10_Rep2_BC_Fwd_07-Rev_09_R2.fastq.gz
Processing file R-50_Rep2_BC_Fwd_08-Rev_09_R1.fastq.gz and R-50_Rep2_BC_Fwd_08-Rev_09_R2.fastq.gz
Processing file R-1_Rep1_BC_Fwd_13-Rev_22_R1.fastq.gz and R-1_Rep1_BC_Fwd_13-Rev_22_R2.fastq.gz
Processing file R-10_Rep1_BC_Fwd_14-Rev_22_R1.fastq.gz and R-10_Rep1_BC_Fwd_14-Rev_22_R2.fastq.gz
Processing file R-50_Rep1_BC_Fwd_15-Rev_22_R1.fastq.gz and R-50_Rep1_BC_Fwd_15-Rev_22_R2.fastq.gz
Processing file R-100_Rep1_BC_Fwd_16-Rev_22_R1.fastq.gz and R-100_Rep1_BC_Fwd_16-Rev_22_R2.fastq.gz
Processing file R-500_Rep1_BC_Fwd_17-Rev_22_R1.fastq.gz and R-500_Rep1_BC_Fwd_17-Rev_22_R2.fastq.gz
Processing file R-1000_Rep1_BC_Fwd_18-Rev_22_R1.fastq.gz and R-1000_Rep1_BC_Fwd_18-Rev_22_R2.fastq.gz
Processing file R-1500_Rep1_BC_Fwd_19-Rev_22_R1.fastq.gz and R-1500_Rep1_BC_Fwd_19-Rev_22_R2.fastq.gz
Processing file R-3000_Rep1_BC_Fwd_20-Rev_22_R1.fastq.gz and R-3000_Rep1_BC_Fwd_20-Rev_22_R2.fastq.gz
Processing marker cpmp
Processing file R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz and R-100_Rep2_BC_Fwd_01-Rev_10_R2.fastq.gz
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'args' in selecting a method for function 'do.call': UserArgumentMismatch
file 'exampleHaplotypR/dePlexMarker/R-100_Rep2_BC_Fwd_01-Rev_10_R1.fastq.gz_F.fastq.gz' exists, but mode is not 'a'