nanopolish call-methylation showing Segmentation fault (core dumped)

[shakti83kumar]

Dear jts,
I want to find methylation in nanopore raw data. I have a computer that has 64GB RAM, 18TB HDD and AMD® Ryzen 9 7950x 16-core processor × 32.
The nanopore data were analysed as mentioned in https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html.
But I got an error at last step "nanopolish call-methylation" as like following:
minimap2 -a -x map-ont /home/shaktikumar/RefGenome/hg38/hg38.fasta
merged_PAY16913_pass_b3c21dcf_78400604.fastq | samtools sort -T tmp -o merged_PAY16913_pass_b3c21dcf_78400604.sorted.bam
[M::mm_idx_gen::24.2681.54] collected minimizers
[M::mm_idx_gen::29.7951.81] sorted minimizers
[M::main::29.7951.81] loaded/built the index for 455 target sequence(s)
[M::mm_mapopt_update::30.7151.79] mid_occ = 728
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 455
[M::mm_idx_stat::31.1351.78] distinct minimizers: 100202295 (37.96% are singletons); average occurrences: 5.732; average spacing: 5.587; total length: 3209286105
[M::worker_pipeline::155.4902.70] mapped 637633 sequences
[M::worker_pipeline::273.6902.84] mapped 632781 sequences
[M::worker_pipeline::379.0852.89] mapped 630885 sequences
[M::worker_pipeline::494.5922.92] mapped 636250 sequences
[M::worker_pipeline::599.0862.94] mapped 634315 sequences
[M::worker_pipeline::717.4812.96] mapped 629061 sequences
[M::worker_pipeline::820.6782.97] mapped 631298 sequences
[M::worker_pipeline::936.0922.97] mapped 634504 sequences
[M::worker_pipeline::1040.0432.98] mapped 633505 sequences
[M::worker_pipeline::1155.8742.98] mapped 635680 sequences
[M::worker_pipeline::1259.2612.99] mapped 635482 sequences
[M::worker_pipeline::1317.099*2.97] mapped 345380 sequences
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -a -x map-ont /home/shaktikumar/RefGenome/hg38/hg38.fasta merged_PAY16913_pass_b3c21dcf_78400604.fastq
[M::main] Real time: 1317.374 sec; CPU: 3915.111 sec; Peak RSS: 11.941 GB
[bam_sort_core] merging from 17 files and 1 in-memory blocks...
shaktikumar@shaktikumar-N7-B650E:/media/shaktikumar/seagate01/ngsdata/DrSwasti/SGPGI_Epitranscriptome/SGPGI/S_T_
27_08_2024_SGPGI/20240827_1825_1C_PAY16913_b3c21dcf$
shaktikumar@shaktikumar-N7-B650E:/media/shaktikumar/seagate01/ngsdata/DrSwasti/SGPGI_Epitranscriptome/SGPGI/S_T_27_08_2024_SGPGI/20240827_1825_1C_PAY16913_b3c21dcf$
shaktikumar@shaktikumar-N7-B650E:/media/shaktikumar/seagate01/ngsdata/DrSwasti/SGPGI_Epitranscriptome/SGPGI/S_T_27_08_2024_SGPGI/20240827_1825_1C_PAY16913_b3c21dcf$ samtools index merged_PAY16913_pass_b3c21dcf_78400604.sorted.bam
shaktikumar@shaktikumar-N7-B650E:/media/shaktikumar/seagate01/ngsdata/DrSwasti/SGPGI_Epitranscriptome/SGPGI/S_T_27_08_2024_SGPGI/20240827_1825_1C_PAY16913_b3c21dcf$ nanopolish call-methylation -t 8 -r merged_PAY16913_pass_b3c21dcf_78400604.fastq -b merged_PAY16913_pass_b3c21dcf_78400604.sorted.bam -g /home/shaktikumar/RefGenome/hg38/hg38.fasta > methylation_calls.tsv
Segmentation fault (core dumped)

[jts]

Hi @shakti83kumar,

It looks like you are trying to call rna modifications using recent (R10.4.1?) data, which nanopolish does not support. If this is the case, I suggest using dorado instead.

Jared

[shakti83kumar]

Dear jts Sir,
you are right. I want call rna modifications. How did you know Sir? Thanks for suggestion. I will try dorado to call RNA modifications. Thanks once again

-- Regards
Shakti Kumar

[jts]

How did you know Sir?

In the screenshots you provided the directory said "Epitranscriptomics"

[shakti83kumar]

Ok ...
Thanks jts Sir.