Not able to run pipeline in google cloud or aws batch

[YussAb]

Ask away!

Dear EPI2ME,

I'm trying to run your pipeline with your demo data. I was able to run the entire pipeline on my local machine. However, I'm not able to run it on google cloud or aws batch. That's strange to me, because I have always been able to run pipelines on cloud after testing it locally. I get stuck with permission errors:

Google:

Error executing process > 'cram_cache (1)'

Caused by:
  Process `cram_cache (1)` terminated with an error exit status (null)

Command executed:

  # Invoke from binary installed to container PATH
  seq_cache_populate.pl -root ref_cache/ demo.fasta
  REF_PATH="ref_cache/%2s/%2s/%s"

Command exit status:
  null

Command output:
  touch: cannot touch '/mnt/disks/genomeupyoussef/DEV/scratch/29/e15c4c08737ec56fba80551948213b/.command.begin': Permission denied/mnt/disks/genomeupyoussef/DEV/scratch/29/e15c4c08737ec56fba80551948213b/.command.run: line 304: /mnt/disks/genomeupyoussef/DEV/scratch/29/e15c4c08737ec56fba80551948213b/.exitcode: Permission denied

Command error:
  cp: cannot create regular file '/mnt/disks/genomeupyoussef/DEV/scratch/29/e15c4c08737ec56fba80551948213b/.command.log': Permission denied

AWS:

Error executing process > 'pipeline:process_references:combine'

Caused by:
  Essential container in task exited

Command executed:

  cat reference_*_.fasta > combined_refs.fasta
  # make sure all sequence IDs are unique
  if [ "$(grep "^>" combined_refs.fasta | sort | uniq -d)" ]; then
      echo "Sequence IDs in the reference files must be unique." 1>&2
      exit 1
  fi
  samtools faidx combined_refs.fasta

Command exit status:
  1

Command output:
  (empty)

Command error:
  mktemp: failed to create directory via template '/tmp/nxf.XXXXXXXXXX': Permission denied
  1:55PM INF shutdown filesystem start
  1:55PM INF shutdown filesystem done

Thanks in advance! best regards, Youssef

[SamStudio8]

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