Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE'

Caused by:
  Process `NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE` terminated with an error exit status (125)


Command executed:

  #!/usr/bin/env Rscript
      suppressPackageStartupMessages(library(dada2))
      suppressPackageStartupMessages(library(digest))
  
      #combine stats files
      for (data in sort(list.files(".", pattern = ".stats.tsv", full.names = TRUE))) {
          if (!exists("stats")){ stats <- read.csv(data, header=TRUE, sep="\t") }
          if (exists("stats")){
              temp <-read.csv(data, header=TRUE, sep="\t")
              stats <-unique(rbind(stats, temp))
              rm(temp)
          }
      }
      write.table( stats, file = "DADA2_stats.tsv", sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE, na = '')
  
      #combine dada-class objects
      files <- sort(list.files(".", pattern = ".ASVtable.rds", full.names = TRUE))
      if ( length(files) == 1 ) {
          ASVtab = readRDS(files[1])
      } else {
          ASVtab <- mergeSequenceTables(tables=files, repeats = "error", orderBy = "abundance", tryRC = FALSE)
      }
      saveRDS(ASVtab, "DADA2_table.rds")
  
      df <- t(ASVtab)
      colnames(df) <- gsub('_1.filt.fastq.gz', '', colnames(df))
      colnames(df) <- gsub('.filt.fastq.gz', '', colnames(df))
      df <- data.frame(sequence = rownames(df), df, check.names=FALSE)
      # Create an md5 sum of the sequences as ASV_ID and rearrange columns
      df$ASV_ID <- sapply(df$sequence, digest, algo='md5', serialize = FALSE)
      df <- df[,c(ncol(df),3:ncol(df)-1,1)]
  
      # file to publish
      write.table(df, file = "DADA2_table.tsv", sep = "\t", row.names = FALSE, quote = FALSE, na = '')
  
      # Write fasta file with ASV sequences to file
      write.table(data.frame(s = sprintf(">%s
  %s", df$ASV_ID, df$sequence)), 'ASV_seqs.fasta', col.names = FALSE, row.names = FALSE, quote = FALSE, na = '')
  
      # Write ASV file with ASV abundances to file
      df$sequence <- NULL
      write.table(df, file = "ASV_table.tsv", sep="\t", row.names = FALSE, quote = FALSE, na = '')
  
      writeLines(c("\"NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE\":", paste0("    R: ", paste0(R.Version()[c("major","minor")], collapse = ".")),paste0("    dada2: ", packageVersion("dada2")) ), "versions.yml")

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' locally
  docker: Error response from daemon: received unexpected HTTP status: 504 Gateway Time-out.
  See 'docker run --help'.

Work dir:
  /home/runner/work/ampliseq/ampliseq/.nf-test/tests/192be031b31e9cc19190a9d9f4a97247/work/23/db08f991e68f1af5870c5f3eb3517b

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/ampliseq/ampliseq/.nf-test/tests/192be031b31e9cc19190a9d9f4a97247/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/ampliseq/ampliseq/.nf-test/tests/192be031b31e9cc19190a9d9f4a97247/meta/nextflow.log' file for details
Nextflow stderr:

Nextflow 24.10.0 is available - Please consider updating your version to it