Pipeline testing on Windows

[KaiZhuPhD]

> devtools::session_info()
- Session info ----------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/Los_Angeles         
 date     2020-11-04                  

- Packages --------------------------------------------------------------------------------------------------
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.3)
 backports     1.1.10  2020-09-15 [1] CRAN (R 4.0.3)
 BiocManager   1.30.10 2019-11-16 [1] CRAN (R 4.0.3)
 callr         3.5.1   2020-10-13 [1] CRAN (R 4.0.3)
 cli           2.1.0   2020-10-12 [1] CRAN (R 4.0.3)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.3)
 desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.3)
 devtools      2.3.2   2020-09-18 [1] CRAN (R 4.0.3)
 digest        0.6.27  2020-10-24 [1] CRAN (R 4.0.3)
 ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.3)
 fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.3)
 fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.3)
 glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.3)
 knitr         1.30    2020-09-22 [1] CRAN (R 4.0.3)
 magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.3)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.3)
 pkgbuild      1.1.0   2020-07-13 [1] CRAN (R 4.0.3)
 pkgload       1.1.0   2020-05-29 [1] CRAN (R 4.0.3)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.3)
 processx      3.4.4   2020-09-03 [1] CRAN (R 4.0.3)
 ps            1.4.0   2020-10-07 [1] CRAN (R 4.0.3)
 R6            2.5.0   2020-10-28 [1] CRAN (R 4.0.3)
 remotes       2.2.0   2020-07-21 [1] CRAN (R 4.0.3)
 rlang         0.4.8   2020-10-08 [1] CRAN (R 4.0.3)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.3)
 rstudioapi    0.11    2020-02-07 [1] CRAN (R 4.0.3)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.3)
 testthat      3.0.0   2020-10-31 [1] CRAN (R 4.0.3)
 usethis       1.6.3   2020-09-17 [1] CRAN (R 4.0.3)
 withr         2.3.0   2020-09-22 [1] CRAN (R 4.0.3)
 xfun          0.19    2020-10-30 [1] CRAN (R 4.0.3)

[1] C:/Users/kai.zhu/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.3/library

[KaiZhuPhD]

Error messages from running ./testing/download-neon-data-metadataworkaround.Rmd:

> source("./code/params.R")
Error in system2("which", args = "cutadapt", stdout = TRUE) : 
  '"which"' not found

> reorganized_files <- organizeRawSequenceData(fn, meta)
Error in organizeRawSequenceData(fn, meta) : 
  All sequencer run ID values are NA. Cannot proceed with reorganizing this download batch.
                              Try a different `fn` or `metadata`.

Also suggest better organized "data" folder.

[KaiZhuPhD]

Error messages from running ./testing/process-16s-sequences-to-seqtabs.Rmd

> source("./code/params.R")
Error in system2("which", args = "cutadapt", stdout = TRUE) : 
  '"which"' not found

The above error makes loading params.R failed. Can't proceed with following steps.

[claraqin]

Hi Kai,

Thanks for posting about this. It seems like a number of people have had a problem with the which command via system2. So I've removed it in the most recent commit. What this does mean, though, is that you will have to find the location of cutadapt on your own file system, and enter it manually into the CUTADAPT_PATH argument in params.R.

[claraqin]

Regarding this error:

> reorganized_files <- organizeRawSequenceData(fn, meta)
Error in organizeRawSequenceData(fn, meta) : 
  All sequencer run ID values are NA. Cannot proceed with reorganizing this download batch.
                              Try a different `fn` or `metadata`.

Could you please print head(fn) and head(meta)?

Also, regarding this:

Also suggest better organized "data" folder.

Which data folder are you referring to? The data subdirectory shouldn't be relevant in the steps that are being tested.

[KaiZhuPhD]

Suggestions:

• Search cutadapt folder and fill in the path in params.R, e.g., https://stackoverflow.com/questions/38291239/using-r-how-do-i-search-for-a-file-folder-on-all-drives-hard-drives-as-well-a
  • On Windows, the path seems to be ~/../AppData/Roaming/Python/Python39/site-packages/cutadapt.
• Create a progress bar for downloading fastq files. Or simply, how many files have been downloaded vs. how many in total.
  • Also reorganized_files <- organizeRawSequenceData(fn, meta) takes long time--suggest creating a progress bar.

No other issues in ./testing/download-neon-data-metadataworkaround.Rmd.

[KaiZhuPhD]

In testing process-its-sequences-to-seqtabs.Rmd, I got the following error message:

trimPrimerITS: No files found at specified location(s) within C:/Users/kai.zhu/Documents/GitHub/NEON_soil_microbe_processing/NEON/raw_sequence/ITS/2_trimmed_mid. Check file path, or post_samplename_pattern argument(s).trimPrimerITS: No files found at specified location(s) within C:/Users/kai.zhu/Documents/GitHub/NEON_soil_microbe_processing/NEON/raw_sequence/ITS/2_trimmed. Check file path, or post_samplename_pattern argument(s).Error in rval[sapply(rval, is.character)] : invalid subscript type 'list'

[claraqin]

Hi Kai,

1. Did you manage to address this issue?

> reorganized_files <- organizeRawSequenceData(fn, meta)
Error in organizeRawSequenceData(fn, meta) : 
  All sequencer run ID values are NA. Cannot proceed with reorganizing this download batch.
                              Try a different `fn` or `metadata`.

2. Regarding this issue:

trimPrimerITS: No files found at specified location(s) within C:/Users/kai.zhu/Documents/GitHub/NEON_soil_microbe_processing/NEON/raw_sequence/ITS/2_trimmed_mid. Check file path, or post_samplename_pattern argument(s).trimPrimerITS: No files found at specified location(s) within C:/Users/kai.zhu/Documents/GitHub/NEON_soil_microbe_processing/NEON/raw_sequence/ITS/2_trimmed. Check file path, or post_samplename_pattern argument(s).Error in rval[sapply(rval, is.character)] : invalid subscript type 'list'

The most likely cause of this, I think, is that your R session wasn't able to find cutadapt. Are you able to check the error logs to see if this error was preceded by "error in running commandsh: ~/.local/bin/cutadapt: No such file or directory"? (If so, you will need to update CUTADAPT_PATH in params.R.)

[claraqin]

The main barrier to using Windows computers to run the processing pipeline was the lack of support for Cutadapt. This is only relevant for the ITS pipeline, and this may be addressed by the Docker container that @rbartelme will soon add to the repo.

I'm leaving this issue open in case any Windows users want to confirm that either (1) the 16S pipeline still works for them, or (2) the Docker container works for them.