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Modkit pileup - segmentation fault and performance issues in high-coverage regions

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#607 3 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
42/100
Tipo de issue
Error
Claridad
Bastante claro
Estado de actividad
Tranquilo
Stack tecnológico
rust
Área
bioinformatics, cli, performance

Línea de trabajo

Start by reproducing the two modkit pileup failures with the supplied commands, including --modified-bases inosine, the high-coverage region, and the comma-separated --region value. Use the reported output to investigate the segmentation fault, low CPU utilization, and contig-missing error. Done means each case has a documented resolution or confirmed workaround, with performance behavior checked on the high-coverage region.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

troubleshooting

Dear ONT staff,

I am working with modkit to profile m6A and inosine in a dRNA-seq sample, and I am encountering a couple of issues.

First, when I try to use the --modified-bases parameter, I encounter a segmentation fault error, with no additional information regarding the cause of the issue.

This is the command I am using:

~/Software/dist_modkit_v0.6.1_481e3c9/modkit pileup
/path/to/aligned/bam
/path/to/output/bed.gz
--reference /path/to/fa.gz
--log /path/to/log
--threads 10
--modified-bases inosine
--region 1

This is the output:

parsing region 1
discarded 0 contigs with zero aligned reads
parsed 1 base modification(s). Base modifications other than 'A:17596' will be counted as 'N_other'.
adding single-base motif: 'A 0'
Segmentation fault (core dumped)

Furthermore, I have a couple of genomic regions covered by ~1M reads (due to high expression of specific transcripts), and this results in the code getting stuck, with only 2 out of 10 CPUs (according to top) being actively used.

This is the output:

parsing region 2
discarded 0 contigs with zero aligned reads
attempting to sample 10042 reads
Threshold of 0.69921875 for base A is low. Consider increasing the filter-percentile or specifying a higher threshold.
using general workers
93037146 B written to output: Test.bed.gz [4.78 MB/s]
[00:00:18] ###############------------------------- 88000000/242193529 genome positions 4,732,930.0021/s 33s
1222798 rows written
0 ~records errored

Could you recommend a workaround to avoid this issue and/or improve performance so that all available CPUs are effectively utilized? I also tried with the --high-depth --max-depth 100 options but it did not help.

Finally, I attempted to skip the two chromosomes with very high coverage. However, when I pass a comma-separated list of chromosome names to the --region option (as suggested in the documentation), I encounter a “contig missing” error.

Thank you very much for your support.

Best regards,

Mattia

Lenguaje dominante
Rust
Estrellas
276
Forks
33
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