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!

[nggvs]

Hi @msubirana ,
I'm not able to reproduce this issue, could you look into lr_microbiome/work/a5/ed6a49a77bb51f2b39869a23be635e
and check if you can view the content of the file with zcat

Thank you very much in advance!

[msubirana]

Hi,

I'm not able

zcat work/a5/ed6a49a77bb51f2b39869a23be635e | head
gzip: work/a5/ed6a49a77bb51f2b39869a23be635e.gz: No such file or directory

[nggvs]

Hi @msubirana,

Could you tell me which version of wf-metagenomics are you using? If it isn't the 2.11.1, could you retry with that one to see if the problem persists? The command you'd need to run is the next one (sorry for not having been so clear in the first message)

# in the directory where you have the "work" directory created by nextflow
 zcat work/a5/ed6a49a77bb51f2b39869a23be635e/input_reads.fastq.gz | head

Also, just to let you know, there is "bug report template" to open an issue.
It asks for some information that is useful to look into it, like for example the version of the workflow or the Operating System, please use this template when reporting some error that you are experiencing.

Thank you very much in advance and for using the workflow!