DECIPHER: Alignment larger than the maximum allowable size

[Charmy0619]

Hi,

I am running pacbio data nad I have trouble in the step of AlignReadsDECIPHER.
Here is the error message:

Error executing process > 'AlignReadsDECIPHER (AlignReadsDECIPHER:R1)'

Caused by:
  Process `AlignReadsDECIPHER (AlignReadsDECIPHER:R1)` terminated with an error exit status (1)

Command executed [/home/qj5/ped_xtan25_chi_link/qj5/test16S_TADA/src/TADA/templates/AlignReadsDECIPHER.R]:

  #!/usr/bin/env Rscript
  .libPaths(c("/mmfs1/home/qj5/R/x86_64-pc-linux-gnu-library/4.4", .libPaths()))
  suppressPackageStartupMessages(library(dada2))
  suppressPackageStartupMessages(library(DECIPHER))
  
  seqs <- readDNAStringSet("asvs.md5.nochim.R1.fna")
  alignment <- AlignSeqs(seqs,
             anchor=NA,
             processors = 64)
  writeXStringSet(alignment, "aligned_seqs.R1.fasta")

Command exit status:
  1

Command output:
  Determining distance matrix based on shared 9-mers:
  ================================================================================
  
  Time difference of 2.04 secs
  
  Clustering into groups by similarity:
  ================================================================================
  
  Time difference of 0.37 secs
  
  Aligning Sequences:
  ================================================================================
  
  Time difference of 949.63 secs
  
  Iteration 1 of 2:
  
  Determining distance matrix based on alignment:
  ================================================================================
  
  Time difference of 1.3 secs
  
  Reclustering into groups by similarity:
  ================================================================================
  
  Time difference of 0.25 secs
  
  Realigning Sequences:
  ===============================================================================

Command error:
  Error in f(p.profile, s.profile) : 
    Alignment larger (6,205,073,628) than the maximum allowable size (2,147,483,647).
  Calls: AlignSeqs -> .align -> do.call -> do.call ->  -> f
  Execution halted

Work dir:
  /mmfs1/projects/ped_xtan25_chi/qj5/16S_pacbio_2024_dam/src/work/15/04113d39009483d31a03e09bfe1530

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

I try to check the "asvs.md5.nochim.R1.fna" files:

seqs <- readDNAStringSet("asvs.md5.nochim.R1.fna")
> # Number of sequences
num_sequences <- length(seqs)
print(num_sequences)
[1] 814

> summary(sequence_lengths)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
   1000    1166    1374    1355    1486    1796
> # Calculate total base pairs (bp) in all sequences
total_bp <- sum(width(seqs))
print(total_bp)
[1] 1102620

I also try to increase the memory to 240G but it's still not working.

Can anyone help?
Thanks.

[cjfields]

@Charmy0619 this is an unusual one. Are you running this on UIUC resources or somewhere else?