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morispi / LEVIATHAN

Linked-reads based structural variant caller with barcode indexing
GNU Affero General Public License v3.0
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Segmentation fault (core dumped) #2

Closed kztyes closed 2 years ago

kztyes commented 3 years ago

After this error, the instruction stopped running. Why？ My bam: Hg002_NA24385
My Ref: hg19 微信图片_20210425100741

morispi commented 3 years ago

Hello,

Segmentation faults are always pretty hard to understand / reproduce without the original data unfortunately. If your dataset is publicly available, could you send my its accession number or a link so I can download it and try to see what's going on?

If not, could you maybe do a samtools view yourBamFile.bam | head so I can try to see if there something wrong with the way your input file is formatted?

Best, Pierre

kztyes commented 3 years ago

Thank you for your quick reply. The data I used is long_read_based, i don't really know if i can use Levithan to detect structural variation. And this is the header of the BAM file I used:

hg002_allreads_ngmlr.2.txt

morispi commented 3 years ago

Oh, if your data is long reads (PacBio, ONT), there is a large chance LEVIATHAN will not manage to perform, indeed. LEVIATHAN has been designed to call SVs on Linked-Reads data, such as 10x Genomics, stLFR, Haplotagging or TELL-Seq. If your reads are not barcoded, there is a huge chance LEVIATHAN will fail to work, indeed.

Sorry if I have not been clear enough, but I would also need some alignments data to better understand what's wrong, and not only the headers. Could you possibly send me another file including some alignments?

Best, Pierre