Error when a trying --amr

[msubirana]

Ask away!

Hi,

I'm running the pipeline like this:

nextflow run epi2me-labs/wf-metagenomics \
--fastq $fastq_pass_path \
-profile singularity \
--database_set PlusPF-8 \
--out_dir $out_dir \
--store_dir $store_dir \
--exclude_host $host_ref \
--amr

And I'm getting this error, any solution? Thanks.

ERROR ~ Error executing process > 'kraken_pipeline:run_amr:abricate (1)'

Caused by:
  Process `kraken_pipeline:run_amr:abricate (1)` terminated with an error exit status (1)

Command executed:

  gunzip -c input_reads.fastq.gz  > input_reads.fastq
  abricate --db resfinder --minid 80 --mincov 80 input_reads.fastq > barcode10_amr_results.tsv

Command exit status:
  1

Command output:
  (empty)

Command error:

  gzip: input_reads.fastq.gz: not in gzip format

Work dir:
 lr_microbiome/work/a5/ed6a49a77bb51f2b39869a23be635e

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

[nggvs]

Hi @msubirana ! Thank you for using the workflow! I'll try to reproduce this issue!