modkit's pileup is unresponsive.

[wjx121]

I have been using modkit's pileup command to generate whole-genome methylation levels; however, after running for 10 hours, no output has been produced. I would appreciate it if anyone could let me know if there is an error in my command.

"minimap2 -ax map-ont myreference all.fastq (bam from dorado to fastq) -y -t 50 | samtools view -o aligned.bam

samtools sort -o aligned.sorted.bam aligned.bam

samtools index aligned.sorted.bam

modkit pileup aligned.sorted.bam ceshi.bed2 --ref myreference -t 50”

discarded 0 contigs with zero aligned reads
attempting to sample 10042 reads
using general workers
[00:00:00] ---------------------------------------- 0/300000000 genome positions 0/s 0s
0 rows written
0 ~records errored

[ArtRand]

Hello @wjx121,

Could you tell me which version of Modkit you're using? I recommend using the latest release, v0.6.1 with the --modified-bases and --reference options. There is an example here.

[wjx121]

Thank you for your help. I am currently using Modkit version v0.6.1.

[ArtRand]

@wjx121 Does the command progress is you use --modified-bases?

[wjx121]

I added the --modified-bases parameter, which resolved the issue within the MoKit software; however, the run completed successfully with 0 reads. I now suspect that my alignment step was incorrect.