Error executing process about nextneopi

[riederd]

Hi,
thanks for your interest in nextNEOpi. I'm sorry you ran into troubles, but it should be easily fixable.

The problem is that you set some incorrect values in the your params.config, i.e.:

  trim_adapters        = true
  adapterSeq           = true // "AGATCGGAAGAG" Illumina Universal Adapter
  adapterSeqR2         = true
  adapterSeqFile       = false // fasta file with adapter seqs

  trim_adapters_RNAseq = true
  adapterSeqRNAseq     = true // "AGATCGGAAGAG"  Illumina Universal Adapter
  adapterSeqR2RNAseq   = true
  adapterSeqFileRNAseq = false // fasta file with adapter seqs

  // extra options for fastp

If you want nextNEOpi to trim adapters, it is enough to set trim_adapters = true and trim_adapters_RNAsq = true, the adapter sequences will be determined automatically. However if you want to explicitly provide adapter sequences you may set

adapterSeq = "YOURADAPTERSEQHERE"
adapterSeqR2 = "YOURADAPTERSEQHERE"
adapterSeqRNAseq = "YOURADAPTERSEQHERE"
adapterSeqR2RNAseq = "YOURADAPTERSEQHERE"

Setting those to true is causing your error, so either set them to your adapter sequences or keep them as false.

[KunFang93]

Thanks for your prompt reply! I follow your suggestion but the pipeline broke with another error😥

Execution cancelled -- Finishing pending tasks before exit
[icbi/nextNEOpi] Pipeline Complete! You can find your results in /scratch/u/kfang/ChenHZ_lab/Neoantigen/test/RESULTS
WARN: WARNING: VEP cache not installed, starting installation. This may take a while.
WARN: WARNING: VEP plugins not installed, starting installation. This may take a while.
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'fastp (Patient353_T1star : tumor_RNA)'

Caused by:
  Process `fastp (Patient353_T1star : tumor_RNA)` terminated with an error exit status (127)

Command executed:

  fastp --thread 4 \
      --in1 OSU13053-0000353-T-0204980-HYB00853-Txome-20190612-Illumina_S1_L004_R1_001.fastq.gz \
      --in2 OSU13053-0000353-T-0204980-HYB00853-Txome-20190612-Illumina_S1_L004_R2_001.fastq.gz \
      --out1 Patient353_T1star_tumor_RNA_trimmed_R1.fastq.gz \
      --out2 Patient353_T1star_tumor_RNA_trimmed_R2.fastq.gz \
      --json Patient353_T1star_tumor_RNA_fastp.json \
       \

Command exit status:
  127

Command output:
  (empty)

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

Work dir:
  /scratch/u/kfang/ChenHZ_lab/Neoantigen/test/work/9a/f94e2c2e9b0bd5ffd50688525c1484

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

If I manually install fastp in the env and run command again, another error will pops up

Error executing process > 'RegionsBedToIntervalList (RegionsBedToIntervalList)'

Caused by:
  Process `RegionsBedToIntervalList (RegionsBedToIntervalList)` terminated with an error exit status (127)

Command executed:

  gatk --java-options -Xmx64G BedToIntervalList \
      -I S07604514_Regions.bed \
      -O S07604514_Regions.interval_list \
      -SD GRCh38.d1.vd1.dict

Command exit status:
  127

Command output:
  (empty)

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

Work dir:
  /data/kun/ChenHZ_lab/Neoantigen/test/work/07/44e34c80c976589a63d643042e9305

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

It looks like the pipeline doesn't find those installed softwares? I wondered how to solve this? Thanks for your time and help!

Best,
Kun

[riederd]

Are you still using -profile conda, if yes, then something went wrong with creating the conda env. I'd need the .nextflow.log file to check.
However, we strongly recommend to use singularity by specifying -profile singularity , conda sometimes results into issues.

[KunFang93]

Yes, I still used -profile conda. I am trying -profile singularity now. It looks good so far!