Amplican doesn't recognize forward reads fast q file
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landenshanie ▴ 40
Last seen 1 day ago

I am trying to use amplican to evaluate nanopore sequencing fastq file of CRISPR'd region. I only have one fastq file for the sample.

I have made the config csv file. However, when running the amplicanPipeline function I get an error that my forward file is blank, but my forward file column contains the name of my fastq file. See screenshot of my config csv below.

# path to example config file
config <-  "~/Desktop/pvol2/Rat_nanopore/try/config_summary_2.csv"
fastq_folder <-"~/Desktop/pvol2/Rat_nanopore/try/W4FBKV_1_678.fastq"  
# output folder, a full path
results_folder <- "~/Desktop/pvol2/Rat_nanopore/try"  
#  run amplican
amplicanPipeline(config,fastq_folder = fastq_folder, results_folder=results_folder,fastqfiles = 1)

Checking write access...
Checking configuration file...
Error in amplicanAlign(config = config, fastq_folder = fastq_folder, use_parallel = use_parallel,  : 
  Forward_Reads_File has empty rows. Change fastqfiles parameter to 2, to operate only on reverse reads.

sessionInfo( )

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/ 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] amplican_1.24.0     data.table_1.14.8   Biostrings_2.70.3  
[4] GenomeInfoDb_1.38.8 XVector_0.42.0      IRanges_2.36.0     
[7] S4Vectors_0.40.2    BiocGenerics_0.48.1

loaded via a namespace (and not attached):
 [1] utf8_1.2.3              generics_0.1.3          bitops_1.0-7           
 [4] stringi_1.7.12          extrafontdb_1.0         digest_0.6.33          
 [7] magrittr_2.0.3          grid_4.3.1              RColorBrewer_1.1-3     
[10] fastmap_1.1.1           plyr_1.8.8              ggthemes_5.1.0         
[13] gridExtra_2.3           purrr_1.0.1             fansi_1.0.4            
[16] waffle_1.0.2            scales_1.2.1            cli_3.6.1              
[19] rlang_1.1.1             crayon_1.5.2            munsell_0.5.0          
[22] tools_4.3.1             dplyr_1.1.2             colorspace_2.1-0       
[25] ggplot2_3.4.2           DT_0.33                 GenomeInfoDbData_1.2.11
[28] curl_5.0.1              vctrs_0.6.3             R6_2.5.1               
[31] lifecycle_1.0.3         zlibbioc_1.48.2         stringr_1.5.0          
[34] htmlwidgets_1.6.2       pkgconfig_2.0.3         pillar_1.9.0           
[37] gtable_0.3.3            glue_1.6.2              Rcpp_1.0.11            
[40] xfun_0.39               tibble_3.2.1            tidyselect_1.2.1       
[43] rstudioapi_0.15.0       knitr_1.43              extrafont_0.19         
[46] htmltools_0.5.5         Rttf2pt1_1.3.12         compiler_4.3.1         
[49] RCurl_1.98-1.12

My config file looks like this:

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