Error: BiocParallel errors

[ThibauldMichel]

Python 3.11.8
Cutadapt 4.6

Cutadapt installed in conda (Bioconda) environment.

Script used: within the R script of the DADA2 pipeline, cutadapt is used as follow.

cutadapt <- "cutadapt" # Path to the executable
for(i in seq_along(fas_Fs_raw)) {
  cat("Processing", "-----------", i, "/", length(fas_Fs_raw), "-----------\n")
  system2(cutadapt, args = c(R1_flags, R2_flags,
                             "--discard-untrimmed",
                             "--max-n 0",
                             # Optional strong constraint on expected length
                             #paste0("-m ", 250-nchar(FWD)[1], ":", 250-nchar(REV)[1]), 
                             #paste0("-M ", 250-nchar(FWD)[1], ":", 250-nchar(REV)[1]), 
                             "-o", fas_Fs_cut[i], "-p", fas_Rs_cut[i],
                             fas_Fs_raw[i], fas_Rs_raw[i]))

Error during processing, we were expecting the creation of an output folder with trimmed reads, but no folder or files are created and there is an error message in the report slurm file (attached).

 WARNING:
    One or more of your adapter sequences may be incomplete.
    Please see the detailed output above.
Stop worker failed with the error: wrong args for environment subassignment
Error: BiocParallel errors
  0 remote errors, element index: 
  154 unevaluated and other errors
  first remote error:
Execution halted

slurm-19692390.txt

[marcelm]

Hi, sorry, but the error in this case is not with Cutadapt itself, so I cannot help. You should probably talk to the BiocParallel or DADA2 developers.

I can only say that you can ignore the 'WARNING: One or more of your adapter sequences may be incomplete' message. This is normal when trimming primers.

[ThibauldMichel]

Thank you @marcelm, I was unaware that the error was caused by something else than Cutadapt.

Nevertheless, Cutadapt is not creating outputs, so I guess another problem is happening preventing the software to work normally.

[marcelm]

What do you mean by "nevertheless"? Do you think there is still a problem in Cutadapt that I can fix? If so, I need to have a way to reproduce the problem for myself, that is, the full command line and an input FASTQ file.

I have never had the problem (myself or reported on the issue tracker) that Cutadapt would not create the output files it is supposed to, so while I’m open to the possibility that something is going wrong, it is most probable to me that something else is preventing you from seeing the files, especially considering that Cutadapt’s logging output shows no error. Since there are other tools involved in the way you use Cutadapt (SLURM, DADA2, BiocParallel), my first guess is that these tools have a bug or are used incorrectly. But I cannot help with that because I have no experience with DADA2.

[ThibauldMichel]

Apologizes, I have miss-used "Nevertheless", I did not want to suggest that cutadapt is causing the problem or asking for any undue fix.
I agree that the problem is probably coming from the rest of the pipeline. It might be as well from the data set, as the same code has work on other similar sets before.
Much thanks for your help.

[marcelm]

Great, then I’ll close the issue. Feel free to comment or open a new issue in case there is something I can do.