Hi!
I've been trying the modkit pileup on both my ONT samples as well as some Pacbio samples, but I've run into an issue with the newer version (v0.6.1) for PB.
For my ONT samples, the pileup from both v0.5.0 and v0.6.1 work fine, no issues. However, when I try modkit pileup with v0.6.1 on pacbio samples the bedmethyl files are empty and it gives me this in the log file:
[modkit-core/src/pileup/subcommand.rs::1489][2026-04-15 10:15:49][ERROR] ~5585761 failed processing
[modkit-core/src/pileup/subcommand.rs::1496][2026-04-15 10:15:49][INFO] Done, processed 0 rows.
No other error messages are visible in the log file so I haven't been able to figure out what to change in my code to make it work.
I've tried both with --phased and without this flag, also tried adding --filter-threshold and --mod-threshold as well as the --use-dynamic workaround. But all of these give me the same line in the log file.
This is my current code, which I also used on the ONT samples:
$modkit pileup \ ${ADJUSTED_BAM_PB} \ ${OUTPUT_BED_PB} \ --ref ${REF} \ --log-filepath ${LOG_PB} \ --threads ${SLURM_CPUS_PER_TASK} \ --modified-bases C:m \ --cpg \ --prefix ${SAMPLE} \ --phased
I also ran the check-tags to make sure it wasn't the MM/ML tags in my bam file, but that came out clean.
I had no issue running the pileup with v0.5.0 on PB samples and other modkit tools (like sample-probs and check-tags) also work fine with version v0.6.1. Only the pileup seems to have an issue.
Do you have any idea what could cause this and how I could fix it so it can run? I am aware this is mostly an ONT tool, but since it worked before I thought it couldn't hurt to ask.
Please let me know if you need any additional info or files from me!
Thanks a lot!
Hi!
I've been trying the modkit pileup on both my ONT samples as well as some Pacbio samples, but I've run into an issue with the newer version (v0.6.1) for PB.
For my ONT samples, the pileup from both v0.5.0 and v0.6.1 work fine, no issues. However, when I try modkit pileup with v0.6.1 on pacbio samples the bedmethyl files are empty and it gives me this in the log file:
No other error messages are visible in the log file so I haven't been able to figure out what to change in my code to make it work.
I've tried both with
--phasedand without this flag, also tried adding--filter-thresholdand--mod-thresholdas well as the--use-dynamicworkaround. But all of these give me the same line in the log file.This is my current code, which I also used on the ONT samples:
$modkit pileup \ ${ADJUSTED_BAM_PB} \ ${OUTPUT_BED_PB} \ --ref ${REF} \ --log-filepath ${LOG_PB} \ --threads ${SLURM_CPUS_PER_TASK} \ --modified-bases C:m \ --cpg \ --prefix ${SAMPLE} \ --phasedI also ran the check-tags to make sure it wasn't the MM/ML tags in my bam file, but that came out clean.
I had no issue running the pileup with v0.5.0 on PB samples and other modkit tools (like sample-probs and check-tags) also work fine with version v0.6.1. Only the pileup seems to have an issue.
Do you have any idea what could cause this and how I could fix it so it can run? I am aware this is mostly an ONT tool, but since it worked before I thought it couldn't hurt to ask.
Please let me know if you need any additional info or files from me!
Thanks a lot!