fastp not found

[ivelsko]

I tried to run madman (on sdag) but got an error that fastp isn't found:

Command: nextflow run maxibor/madman --reads '/projects1/microbiome_calculus/abpCapture/04-analysis/AB_assembly/set1/input/ancient/ECO*.AB1.1_S0_L005_R{1,2}_001.fastq.gz' --metaspades

Error:

-[nf-core/madman] Pipeline completed with errors-
WARN: Killing pending tasks (4)
Error executing process > 'PRE_ASSEMBLY:fastp (ECO002.B0101)'

Caused by:
  Process `PRE_ASSEMBLY:fastp (ECO002.B0101)` terminated with an error exit status (127)

Command executed:

  fastp --in1 ECO002.B0101.pair1.trimmed.fastq --in2 ECO002.B0101.pair2.trimmed.fastq --out1 ECO002.B0101.pair1.trimmed.fq.gz --out2 ECO002.B0101.pair2.trimmed.fq.gz -A -g --poly_g_min_len "10" -Q -L -w 6 --json ECO002.B0101.json

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: fastp: command not found

Work dir:
  /projects1/microbiome_calculus/abpCapture/04-analysis/AB_assembly/set1/madman/test_ancient/work/da/d78f08e5568099c4ccf5fd64a16024

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

But I shouldn't need to separately download fastp, right?

[jfy133]

Don't you need a -profile? (This is what normally specifies a software environment, unless everything is installed locally)

[ivelsko]

Ah yes, that fixed it