I have been facing several different failing fetchngs runs when using sratools, the error seems to be always similar to this:

Error executing process > 'NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX3445732_SRR6348978)'

Caused by:
  Essential container in task exited

Command executed:

  export NCBI_SETTINGS="$PWD/user-settings.mkfg"
  
  fasterq-dump \
      --split-files --include-technical \
      --threads 6 \
      --outfile SRX3445732_SRR6348978 \
       \
      SRR6348978
  
  pigz \
       \
      --no-name \
      --processes 6 \
      *.fastq
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP":
      sratools: $(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  spots read      : 339,247,891
  reads read      : 339,247,891
  reads written   : 339,247,891
  pigz: skipping: *.fastq does not exist
  3:24PM INF shutdown filesystem start
  3:25PM INF shutdown filesystem done

So it appears that

fasterq-dump

has successfully extracted reads, but

pigz

then dies as there are no files called

.fastq

, is that correct? I went to the work directory where of the failed process, here are the contents:

fasterq.tmp.ip/
2024-03-20 15:05:58          0 
2024-03-20 15:06:13          0 .command.begin
2024-03-20 15:24:32        129 .command.err
2024-03-20 15:24:32        129 .command.log
2024-03-20 15:25:38          0 .command.out
2024-03-20 15:05:58      11027 .command.run
2024-03-20 15:05:58        528 .command.sh
2024-03-20 15:06:13          0 .command.trace
2024-03-20 15:24:32          1 .exitcode
2024-03-20 15:25:25    4263995 .fusion.log
2024-03-20 15:24:32         29 .fusion.symlinks
2024-03-20 15:24:32         96 SRR6348978
2024-03-20 15:24:34 95223460854 SRX3445732_SRR6348978
2024-03-20 15:24:32        104 user-settings.mkfg

That SRX… files is indeed in FastQ format:

head SRX3445732_SRR6348978
@SRR6348978.1 1 length=98
TTGTACTAAGGTCAAATCTAAGTGGATTAAGGAACTCCACATAAAACCAGAGACACTGAAACTTACAGAGGAGAAAGTAGGGAAAAGCCTCGAAGATA
+SRR6348978.1 1 length=98
A<7F<JFJJJFJJJJJJJJJJJAFAJFJJJJJJJFJJJJJJJJJJJJJJFFFJFJFFFJJJJFJ<JFJFFJFJJJFJFFJFJJJJFJJ<JFFFJJJJF
@SRR6348978.2 2 length=98
CCAGGTCCATCCATTTGGCTAGGAATTTCATAAATTCATTCTTTTTAATAGCTGAGTAGTACTCCATTGTGTAGATCTACCACATTTTCTGTATCCAT
+SRR6348978.2 2 length=98
A<FFFJJJJJJJJFJJJJJJJJJFJFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJFFJJJJJJJFJJJJ-A----77A<--<7-7------

Any clues on how to make this work?