learnErrors can't find files

[arkaryote]

I've come to a halt in my tutorial of dada2 due to issues with learnErrors.
errF <- learnErrors(filtFs, multithread=F) errR <- learnErrors(filtRs, multithread=F)
Error in derepFastq(fls[[i]], qualityType = qualityType) : Not all provided files exist.

I double checked if all my files listed in the filtFs object match what's in my path; they do. I'm sorry if this is a very rudimentary issue and if it's already been addressed, I was unable to find anything that addressed this.

`sessionInfo()

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] patchwork_0.0.1 dada2_1.12.1 Rcpp_1.0.2

loaded via a namespace (and not attached):
[1] plyr_1.8.4 RColorBrewer_1.1-2 pillar_1.4.2 compiler_3.6.0 GenomeInfoDb_1.20.0 XVector_0.24.0
[7] bitops_1.0-6 tools_3.6.0 zlibbioc_1.30.0 tibble_2.1.3 gtable_0.3.0 lattice_0.20-38
[13] pkgconfig_2.0.2 rlang_0.4.0 Matrix_1.2-17 DelayedArray_0.10.0 rstudioapi_0.10 parallel_3.6.0
[19] GenomeInfoDbData_1.2.1 stringr_1.4.0 hwriter_1.3.2 Biostrings_2.52.0 S4Vectors_0.22.0 IRanges_2.18.1
[25] stats4_3.6.0 grid_3.6.0 Biobase_2.44.0 BiocParallel_1.18.1 latticeExtra_0.6-28 magrittr_1.5
[31] reshape2_1.4.3 ggplot2_3.2.1 scales_1.0.0 Rsamtools_2.0.0 matrixStats_0.54.0 BiocGenerics_0.30.0
[37] GenomicRanges_1.36.0 GenomicAlignments_1.20.1 ShortRead_1.42.0 SummarizedExperiment_1.14.1 colorspace_1.4-1 labeling_0.3
[43] stringi_1.4.3 RCurl_1.95-4.12 RcppParallel_4.4.3 lazyeval_0.2.2 munsell_0.5.0 crayon_1.3.4 `

[benjjneb]

What are the results of table(file.exists(filtFs)) and table(file.exists(filtRs))?

[arkaryote]

Thank you for the response. After the filterandTrim command, both the F and R reads had 2 missing (re-iterated by your suggestion). I tried to skip to the next step and I got a message commenting that some of the files were empty or had no reads. After manually removing those 4 files from the directory and re-running the codes, everything was successful.