Multiple issues: config parsing errors, script variable undefined, and OOM in create_kmers_database

[txfc]

I encountered a series of problems when trying to run RFHap on my trio dataset (paternal/maternal Illumina short reads, child ont long reads). After resolving initial configuration and script syntax errors, the pipeline still fails at the create_kmers_database step due to kmc_tools subtract being killed by the OOM killer. Below I detail each issue and the workarounds I applied, hoping for improvements in the pipeline.

Environment

Nextflow version: 26.04.3

Singularity version: (latest)

Resource: 256 CPU cores, 1000 GB RAM (but create_kmers_database still OOM with default settings)

Steps to reproduce

Clone RFHap repository.

Prepare input text files (paternal.txt, maternal.txt, child.txt) each containing a CSV header path and one line with the file path.

Run the pipeline with:

nextflow run rfhap.nf --paternal_reads paternal.txt --maternal_reads maternal.txt --child_reads child.txt --num_cases 400000 --outdir results -profile local

Issue 1: Nextflow config parsing error

The provided nextflow.config contained a line:

groovy
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss' )
Inside a configuration block, using def is not allowed and leads to:

text
Variable declarations cannot be mixed with config statements
Workaround: I changed it to:

groovy
trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss' )
and added params.trace_timestamp = ... where needed. This allowed the config to be parsed.

Issue 2: Script variable undefined in rfhap.nf

Two variables were not defined, causing compilation errors:

In help_function(): help was assigned without def.

In process predictRF: filename was used inside the script but never defined.

Error messages:

text

Error rfhap.nf:7:5: `help` was assigned but not declared
Error rfhap.nf:208:13: `filename` is not defined
Workaround: I added def to help inside the function and defined def filename = matrix.baseName at the beginning of the script block in predictRF. After these changes the pipeline started.

Issue 3: OOM in create_kmers_database (kmc_tools subtract killed)

After fixing the above, the pipeline ran for ~2 days and then failed at the create_kmers_database step. The error log shows:

Launching `rfhap/rfhap.nf` [loving_allen] revision: 5f660f3037

executor >  local (4)
[66/dfa18d] create_kmers_database (2) | 0 of 4
[-        ] print_paths               -
[-        ] sort_kmer_db              -
[-        ] FastKM                    -
[-        ] trainRF                   -
[-        ] predictRF                 -
[-        ] setHaplotypes             -
[-        ] seqtk                     -
WARN: Killing running tasks (3)
ERROR ~ Error executing process > 'create_kmers_database (4)'

Caused by:
  Process `create_kmers_database (4)` terminated with an error exit status (1)


Command executed:

  mkdir uk33                                                                                                     /home/duanying/refgenome_assembly/rfhap/aux_scripts/find_unique_kmers.py -k33 -p  100 -o uk33 --path-to-kmc kmc B685_1_merge.fq.gz,B685_2_merge.fq.gz B54_1_merge.fq.gz,B54_2_merge.fq.gz > uk33/uk33.log.txt 2> uk33/uk33.err.txt

Command exit status:
  1

Command output:
  (empty)

Command error:                                                                                                   INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred

Work dir:
  /home/duanying/refgenome_assembly/work/f7/7938811751e1519fb91516395cd89e

Container:                                                                                                       /home/duanying/refgenome_assembly/work/singularity/community.wave.seqera.io-library-kmc_mappy_seqtk_r-caret_pruned-46de1e7eb6bf9c6d.img
                                                                                                               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
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details

Thank you for your work on RFHap!