Segmentation Fault on Test File

fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing

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Segmentation Fault on Test File #138

Closed mcfarland-k closed 5 years ago

mcfarland-k commented 5 years ago

Hi Fritz, I am getting a segmentation fault when running the test case on my cluster.

I compiled with gcc/g++ version 4.8.5.

When running the test case sniffles -m reads_region.bam -v test., I get the following

Estimating parameter...

    Max dist between aln events: 4

    Max diff in window: 50

    Min score ratio: 2

    Avg DEL ratio: 0.0432235

    Avg INS ratio: 0.0740733`

Start parsing... 21

    Switch Chr 21

Finalizing  ..

Segmentation fault

I've tried recompiling with newer versions of GNU compilers (v5 and 6), but haven't been successful.

Any help would be much appreciated.

Kevin McFarland Johns Hopkins University Chemical & Biomolecular Engineering

fritzsedlazeck commented 5 years ago

I dont think it has something to do with the compiling. Can you check if you have permission to write the output file? Thanks for reaching out. Fritz

mcfarland-k commented 5 years ago

Not completely clear on what you mean for permission to write the output file, but I checked my permissions for the folder, and I have write access. Just to be sure, I used chmod 777 for the files, and also attempted to copy the files and run them outside of the test folder. Both of them gave me the same output I posted above. Kevin

fritzsedlazeck commented 5 years ago

Mhm this is tricky. Usually, you get that kind of an error when Sniffles tries to write something out and fails to do so. I just tried it again with the test case and the newest code: Screen Shot 2019-04-02 at 11 36 06 AM

Is it on Marc or is it on a different environment? Thanks Fritz

mcfarland-k commented 5 years ago

I see, not sure why it would be doing it for me. Yes, it's on marcc. Best, Kevin

fritzsedlazeck commented 5 years ago

can you go to wherever you start sniffles from and do atouch test ?

fritzsedlazeck commented 5 years ago

I also assumbed you cloned the code from the git?

mcfarland-k commented 5 years ago

Touch test worked, and I indeed cloned from git.

fritzsedlazeck commented 5 years ago

Mhm let me think about this a bit.... I pinged a friend at JHU if he can have a look... I am running out of ideas. Thanks Fritz

mcfarland-k commented 5 years ago

Okay, thank you very much for your help and responsiveness!

malonge commented 5 years ago

You can email me at malonge11@gmail.com

Perhaps I can test things out on MARCC

ttian627 commented 5 years ago

I have the same problem. Has it been solved?

fritzsedlazeck commented 5 years ago

No it hasnt. My problem is that I cannot reproduce it. I will try on different machines, but so far I was not lucky...

fritzsedlazeck commented 5 years ago

@ttian627 can you post your command line output?

ttian627 commented 5 years ago

This is my command line output [ttian@localhost test_set]$ ../bin/sniffles-core-1.0.11/sniffles -m reads_region.bam -v test.vcf Estimating parameter... Max dist between aln events: 4 Max diff in window: 50 Min score ratio: 2 Avg DEL ratio: 0.0432235 Avg INS ratio: 0.0740733 Start parsing... 21 Switch Chr 21 Finalizing .. Segmentation fault (core dumped)

fritzsedlazeck commented 5 years ago

Ok I think I found something that I recently changed at this location, which could effect this. Could someone clone the code again, rebuild and test? Thanks Fritz

ttian627 commented 5 years ago

It works, thank you very much!

fritzsedlazeck commented 5 years ago

Awesome. Thanks to everyone and sorry that it took so long.

mcfarland-k commented 5 years ago

Thanks again for your help Fritz!

Kevin