Tool output differs from expected

[WilliamChen9999]

Description of the bug

Thanks for the pipeline!
I was testing this pipeline with my data, but a error occurred and the pipeline was failed. After alignment, it created a ....combined.bed.gz file. But the next step required a input of ....hap1.bed.gz. The output from previous step mismatched the expected input for next step. How could I fixed this issue?

Command used and terminal output

[2026-06-30][23:36:59][aligned_bam_to_cpg_scores][INFO] Processing alignment file 'sorted_bc2095_tagged.bam'
  [2026-06-30][23:39:18][aligned_bam_to_cpg_scores][INFO] Finished processing alignment files.
  [2026-06-30][23:39:18][aligned_bam_to_cpg_scores][INFO] Writing combined site methylation to bigwig file: 'bc2095.combin                                                                                    ed.bw'
  [2026-06-30][23:39:18][aligned_bam_to_cpg_scores][INFO] Writing combined site methylation to bed file: 'bc2095.combined.                                                                                    bed.gz'
  [2026-06-30][23:39:18][aligned_bam_to_cpg_scores][INFO] aligned_bam_to_cpg_scores completed. Total Runtime: 00:02:24.94
  mv: cannot stat 'bc2095.hap1.bed.gz': No such file or directory

Relevant files

No response

System information

No response

[YiJin-Xiong]

Hi @WilliamChen9999,

Thanks for reporting this issue.

In nf-core/methylong, pb-CpG-tools generates the hap1 and hap2 outputs only when the corresponding HP-tagged read groups contain sufficient valid methylation data.

The absence of a hap1 or hap2 output may be caused by several factors, for example:

• no reads, or very few reads, were assigned to one of the HP groups;
• the methylation sites did not meet the minimum coverage or mapping quality requirements.

Could you please provide the complete nf-core/methylong command you used?

It would also be helpful if you could provide the .command.sh and .command.log files from the work directory.

Thanks again for reporting this issue.

[WilliamChen9999]

Hi @WilliamChen9999,

Thanks for reporting this issue.

In nf-core/methylong, pb-CpG-tools generates the hap1 and hap2 outputs only when the corresponding HP-tagged read groups contain sufficient valid methylation data.

The absence of a hap1 or hap2 output may be caused by several factors, for example:

• no reads, or very few reads, were assigned to one of the HP groups;
• the methylation sites did not meet the minimum coverage or mapping quality requirements.

Could you please provide the complete nf-core/methylong command you used?

It would also be helpful if you could provide the .command.sh and .command.log files from the work directory.

Thanks again for reporting this issue.

Hi YiJin,

Thanks a lot for your reply.

The command I used to run nf-core/methylong was:
nextflow run nf-core/methylong -r 2.0.0 -params-file nf-params.json -profile unsw_katana -resume

The contents of nf-params.json are:
{
"input": "xxx/longreadtest/samplesheet.csv",
"outdir": "xxx/longreadtest/result",
"pacbio_modcall": true,
"pileup_count": true
}

I have attached the requested .command.sh and .command.log files.

Please let me know if you need any additional information.

Best,
William

.command.log
.command.sh

[YiJin-Xiong]

Hi @WilliamChen9999,

Thanks for providing the command and log files.

As mentioned previously, pb-CpG-tools applies relatively strict coverage requirements. The strand-specific HP groups in this dataset may not contain sufficient valid data, which is why no hap1 or hap2 output was generated.

We therefore recommend using Modkit for methylation pileup instead. You can add the following parameter to your command:

--pileup_method modkit

Alternatively, add the following entry to your nf-params.json file:

"pileup_method": "modkit"