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quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data
MIT License
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SIGSEGV: Illegal storage access. (Attempt to read from nil?) #25

Closed bjtrost closed 3 years ago

bjtrost commented 5 years ago

I am testing STRling for the first time, and am getting the following error message at the "call" step. The "extract" step seems to run fine. Here is the stderr output from the call step:

[strling] read 1130403 treads from bin file
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

And in case it helps, here is the same from the extract step:

[strling] finding STR regions on reference chromosome: chr1
[strling] finding STR regions on reference chromosome: chr2
[strling] finding STR regions on reference chromosome: chr3
[strling] finding STR regions on reference chromosome: chr4
[strling] finding STR regions on reference chromosome: chr5
[strling] finding STR regions on reference chromosome: chr6
[strling] finding STR regions on reference chromosome: chr7
[strling] finding STR regions on reference chromosome: chr8
[strling] finding STR regions on reference chromosome: chr9
[strling] finding STR regions on reference chromosome: chr10
[strling] finding STR regions on reference chromosome: chr11
[strling] finding STR regions on reference chromosome: chr12
[strling] finding STR regions on reference chromosome: chr13
[strling] finding STR regions on reference chromosome: chr14
[strling] finding STR regions on reference chromosome: chr15
[strling] finding STR regions on reference chromosome: chr16
[strling] finding STR regions on reference chromosome: chr17
[strling] finding STR regions on reference chromosome: chr18
[strling] finding STR regions on reference chromosome: chr19
[strling] finding STR regions on reference chromosome: chr20
[strling] finding STR regions on reference chromosome: chr21
[strling] finding STR regions on reference chromosome: chr22
[strling] finding STR regions on reference chromosome: chrX
[strling] finding STR regions on reference chromosome: chrY
[strling] finding STR regions on reference chromosome: chr6_GL000250v2_alt
[strling] finding STR regions on reference chromosome: chr16_KI270853v1_alt
[strling] finding STR regions on reference chromosome: chr17_KI270857v1_alt
[strling] finding STR regions on reference chromosome: chr6_GL000251v2_alt
[strling] finding STR regions on reference chromosome: chr15_KI270905v1_alt
[strling] finding STR regions on reference chromosome: chr6_GL000252v2_alt
[strling] finding STR regions on reference chromosome: chr6_GL000253v2_alt
[strling] finding STR regions on reference chromosome: chr6_GL000254v2_alt
[strling] finding STR regions on reference chromosome: chr6_GL000255v2_alt
[strling] finding STR regions on reference chromosome: chr6_GL000256v2_alt
[strling] found 3470 STR-like regions in the genome
[strling] got STR repeats from genome into an interval tree
[strling] collecting str-like reads
[strling] extracting chromosome:chr1
[strling] extracting chromosome:chr2
[strling] extracting chromosome:chr3
[strling] extracting chromosome:chr4
[strling] extracting chromosome:chr5
[strling] extracting chromosome:chr6
[strling] extracting chromosome:chr7
[strling] extracting chromosome:chr8
[strling] extracting chromosome:chr9
[strling] extracting chromosome:chr10
[strling] extracting chromosome:chr11
[strling] extracting chromosome:chr12
[strling] extracting chromosome:chr13
[strling] extracting chromosome:chr14
[strling] extracting chromosome:chr15
[strling] extracting chromosome:chr16
[strling] extracting chromosome:chr17
[strling] extracting chromosome:chr18
[strling] extracting chromosome:chr19
[strling] extracting chromosome:chr20
[strling] extracting chromosome:chr21
[strling] extracting chromosome:chr22
[strling] extracting chromosome:chrX
[strling] extracting chromosome:chrY
[strling] extracting chromosome:chr6_GL000250v2_alt
[strling] extracting chromosome:chr16_KI270853v1_alt
[strling] extracting chromosome:chr17_KI270857v1_alt
[strling] extracting chromosome:chr6_GL000251v2_alt
[strling] extracting chromosome:chr15_KI270905v1_alt
[strling] extracting chromosome:chr6_GL000252v2_alt
[strling] extracting chromosome:chr6_GL000253v2_alt
[strling] extracting chromosome:chr6_GL000254v2_alt
[strling] extracting chromosome:chr6_GL000255v2_alt
[strling] extracting chromosome:chr6_GL000256v2_alt
[strling] extracting unampped reads
[strling] writing binary file:HuRef.bin
[strling] finished extraction

I am running it on a BAM file aligned to hg38.

brentp commented 5 years ago

hi, thanks for trying it out and reporting. I have updated the release page to include a debug binary that will give us more information. would you run that on the call step and report the output?

bjtrost commented 5 years ago

Thanks. Here's what I got this time for the call step:

[strling] read 1130403 treads from bin file
Traceback (most recent call last)
/home/brentp/src/strling/src/strling.nim(33) strling
/home/brentp/src/strling/src/strling.nim(30) main
/home/brentp/src/strling/src/strpkg/call.nim(168) call_main
/root/.nimble/pkgs/hts-0.2.23/hts/bam.nim(251) spanners
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
brentp commented 5 years ago

hmm. nothing obvious. could you verify that you're using the correct reference and could you try re-indexing your bam? any change you could share the bam file offline?

bjtrost commented 4 years ago

I tried a second BAM (actually CRAM) file, and it worked. The BAM file and the CRAM file were generated using slightly different pipelines. I'm not sure where the difference might lie. I will e-mail you instructions for downloading the non-working BAM file via SFTP.

hdashnow commented 4 years ago

Did we ever sort out this error message?

58 might be related, and was fixed in the latest release, if you'd like to have another try: https://github.com/quinlan-lab/STRling/releases/tag/v0.2.1

hdashnow commented 3 years ago

Closing. Feel free to reopen if the issue persists in the latest version.