A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Has anyone ecountered this error before ?


```ERROR ~ Error executing process > 'NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT (group-0)'

Caused by:
  Process `... MEGAHIT (group-0)` terminated with an error exit status (1)

Command executed:

  megahit \
      --mem-util 0.9 \
      -t 24 \
      -r group0.fastq.gz \
      --out-prefix MEGAHIT-group-0
...
Command exit status:
  1

Command error:
  megahit: MEGAHIT v1.2.9
  option --mem-util not recognized```

Do you mean

```    --mem-flag               &lt;int&gt;          SdBG builder memory mode. 0: minimum; 1: moderate;
                                            others: use all memory specified by '-m/--memory' [1]```
?

I don't know what is it, I got this error :

```Caused by:
  Process `NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT (group-0)` terminated with an error exit status (1)


Command executed:

  megahit \
      --mem-util 0.9 \
      -t 24 \
      -r group0.fastq.gz \
      --out-prefix MEGAHIT-group-0

  pigz \
      --no-name \
      -p 24 \
       \
      megahit_out/*.fa \
      megahit_out/intermediate_contigs/*.fa

  mv megahit_out/* .

  cat &lt;&lt;-END_VERSIONS &gt; versions.yml
  "NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT":
      megahit: $(echo $(megahit -v 2&gt;&amp;1) | sed 's/MEGAHIT v//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  megahit: MEGAHIT v1.2.9
  option --mem-util not recognized

Work dir:
  /home/rladeira/etude_flamme/mag/work/ef/98bb4587c443b07b08fd0e2cb076e7

Container:
  /home/rladeira/etude_rfx/ampliseq/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-f2-f2cb827988dca7067ff8096c37cb20bc841c878013da52ad47a50865d54efe83-data.img

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

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

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

`--mem-util` is not referred to anywhere in our code base, so you must be somehow be suppliying.

I also see something very weird - why is your container from `ampliseq` :thinking_face:

Ok, sorry it's coming from an error in my config file, sorry !