modkit (0.6.4) pileup - Segmentation fault
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评估
- 难度
- 4/5
- 预计耗时
- 3-5 天
- 新手友好度
- 48/100
- Issue 类型
- 缺陷
- 描述清晰度
- 基本清楚
- 活跃度
- 活跃
- 技术栈
- rust
- 领域
- bioinformatics, cli
调研方向
Start by reproducing the crash with modkit 0.6.4 using pileup on the reported modBAM, reference, --modified-bases values, and --allow-non-primary option; compare with the successful command that omits those options. The issue does not name source files or tests, so trace the pileup path that parses these options and handles non-primary alignments. Done means the same input completes without a segmentation fault and produces pileup output.
由索引模型根据 Issue 内容生成。
描述
Dear modkit developers,
I am encountering a "Segmentation fault (core dumped)" error when running modkit pileup on a modBAM file with the --modified-bases and --allow-non-primary options.
This issue does not seem related to a specific mark or the number of threads used. It occurs both when working with a single chromosome and when processing the entire genome. However, omitting the two options mentioned above allows the process to run smoothly.
Could you please help me resolve this issue?
Thank you and best regards,
Mattia
(base) [mfurlan@cnode01 pipelines]$ ${modkitPath}/modkit pileup
${BAMsPaths}/minimap2_filtered.bam
${ResultsPath}/${chr}_pileup.output.bed
--region ${chr}
--threads 1
parsing region chr21
discarded 0 contigs with zero aligned reads
attempting to sample at least 10042 reads
calculating threshold value with probabilites from reads
setting threshold 0.6855469 (qual: 175) for base C, percentile 10, 125760 total probabilites
setting threshold 0.7207031 (qual: 184) for base T, percentile 10, 161779 total probabilites
setting threshold 0.8925781 (qual: 228) for base G, percentile 10, 134269 total probabilites
setting threshold 0.6464844 (qual: 165) for base A, percentile 10, 190579 total probabilites
using general workers
Done, processed 334986 rows.
(base) [mfurlan@cnode01 pipelines]$ head ${ResultsPath}/${chr}_pileup.output.bed
chr21 5035650 5035651 19229 1 + 5035650 5035651 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035651 5035652 19229 1 + 5035651 5035652 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035652 5035653 m 1 + 5035652 5035653 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035652 5035653 19228 1 + 5035652 5035653 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035653 5035654 a 1 + 5035653 5035654 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035653 5035654 17596 1 + 5035653 5035654 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035653 5035654 69426 1 + 5035653 5035654 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035654 5035655 19229 1 + 5035654 5035655 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035655 5035656 17802 1 + 5035655 5035656 255,0,0 1 0.00 0 1 0 0 0 0 0
chr21 5035655 5035656 19227 1 + 5035655 5035656 255,0,0 1 0.00 0 1 0 0 0 0 0
(base) [mfurlan@cnode01 pipelines]$ ${modkitPath}/modkit pileup
${BAMsPaths}/minimap2_filtered.bam
${ResultsPath}/${chr}_pileup.output.bed
--region ${chr}
--threads 1
--reference ${genomeFastaPath}
--modified-bases C:m A:a A:17596 T:17802 C:19228 A:69426 G:19229 T:19227
--allow-non-primary
parsing region chr21
discarded 0 contigs with zero aligned reads
parsed 8 base modification(s). Base modifications other than 'A:17596,A:69426,A:a,C:19228,C:m,G:19229,T:17802,T:19227' will be counted as 'N_other'.
adding single-base motif: 'A 0'
adding single-base motif: 'C 0'
adding single-base motif: 'G 0'
adding single-base motif: 'T 0'
0 B written to output: chr21_pileup.output.bed [0 B/s] Segmentation fault (core dumped)
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