search

valenlab / amplican

9 stars 4 forks source link

forward reads file has empty rows error #20

Open shanie-landen opened 3 weeks ago

shanie-landen commented 3 weeks ago

Hello,

I only have one fastq file for the sample. 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 code, error, and screenshot of my config csv below.

config <-  "~/Desktop/pvol2/Rat_nanopore/try/config_summary_2.csv"
fastq_folder <-"~/Desktop/pvol2/Rat_nanopore/try/W4FBKV_1_678.fastq"  
results_folder <- "~/Desktop/pvol2/Rat_nanopore/try"  
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/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

screesnhotconfig

Thanks!

JokingHero commented 3 weeks ago

Your fastq folder is a path to the fastq file. It should be something like this:

fastq_folder <-"~/Desktop/pvol2/Rat_nanopore/try/"

shanie-landen commented 3 weeks ago

Hi Kornel

Thanks for your reply. I have tried this as well and get a different error:

setwd("/pvol2/Rat_nanopore/try")config <- "~/Desktop/pvol2/Rat_nanopore/try/"fastq_folder <-"~/Desktop/pvol2/Rat_nanopore/try/"results_folder <- "~/Desktop/pvol2/Rat_nanopore/try/results/"amplicanPipeline(config, fastq_folder, results_folder)Checking write access... Checking configuration file... Error in data.table::fread(config) : File '/pvol2/Rat_nanopore/try' is a directory. Not yet implemented.

Thanks for your help

Shanie

On Tue, Jun 11, 2024 at 8:47 PM Kornel Labun @.***> wrote:

Your fastq folder is a path to the fastq file. It should be something like this:

fastq_folder <-"~/Desktop/pvol2/Rat_nanopore/try/"

— Reply to this email directly, view it on GitHub https://github.com/valenlab/amplican/issues/20#issuecomment-2160434488, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASRYN5DUN6WNMZLZO7RBGB3ZG3ITTAVCNFSM6AAAAABJBADN5KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRQGQZTINBYHA . You are receiving this because you authored the thread.Message ID: @.***>

JokingHero commented 3 weeks ago

The error perfectly shows you what is wrong...

setwd("~/Desktop//pvol2/Rat_nanopore/try/") config <- "./config_summary_2.csv" fastq_folder <- "./" results_folder <- "./results/"

shanie-landen commented 3 weeks ago

Hi Kornel,

Disregard my emails, I am working through the errors, will see how I go. Thanks for your help.

Best Shanie

On Wed, Jun 12, 2024 at 2:45 AM Shanie Landen @.***> wrote:

Hi Kornel

Please disregard my last email and sorry to bug you with so many attempts... I have tried the last code you sent and fixed something in my config file (attached it for reference) but still getting an error:

setwd("/pvol2/Rat_nanopore/try/")> config <- "./config_summary.csv"> fastq_folder <- "./"> results_folder <- "./results/"> amplicanPipeline(config,fastq_folder, results_folder,fastqfiles = 1)Checking write access... Checking configuration file... Error in checkConfigFile(cfgT, fastq_folder) : Config file has bad rows: 2 due to NA/NULL values

Best

Shanie

On Tue, Jun 11, 2024 at 10:16 PM Shanie Landen @.***> wrote:

I have tried this as well, I get the same as the first error, see below. Perhaps I've made a mistake in my config file? I have attached it. I really appreciate your help, I am quite looking forward to the results...

amplicanPipeline(config,fastq_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.

On Tue, Jun 11, 2024 at 9:21 PM Kornel Labun @.***> wrote:

The error perfectly shows you what is wrong...

setwd("/pvol2/Rat_nanopore/try/") config <- "./config_summary_2.csv" fastq_folder <- "./" results_folder <- "./results/"

— Reply to this email directly, view it on GitHub https://github.com/valenlab/amplican/issues/20#issuecomment-2160495622, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASRYN5ETJRNZIL34F7UHGO3ZG3MVLAVCNFSM6AAAAABJBADN5KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRQGQ4TKNRSGI . You are receiving this because you authored the thread.Message ID: @.***>