Error with merging paired ends using mergeAmpliconReads() #18
Description
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!