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sfu-compbio / sinvict

SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
http://sfu-compbio.github.io/sinvict
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Segmentation fault error #6

Closed HaoKuo closed 7 years ago

HaoKuo commented 7 years ago

Hi~ I encountered an error when i ran sinvict using command like : ./sinvict -t readcount_dir/ -o test

Segmentation fault (core dumped)

./sinvict -h went well.

Any help about that? Thanks a lot~

ckockan commented 7 years ago

Hi, that sounds like a directory/file issue to me. Can you try using absolute paths for -t and -o and see if that works? Also, the readcount_dir should only contain the actual readcount files and nothing else, so that might be the problem too. For instance, if your readcount_dir is "/home/some_project/some_experiment/readcount_dir", that directory should only contain files such as sample1.readcount, sample2.readcount, etc.

HaoKuo commented 7 years ago

Thanks ckockan~ I've tried the absolute paths for -t and -o and got same error "Segmentation fault (core dumped)". There is only one test.readcount (20 lines) in the directory /home/some_project/some_experiment/readcount_dir Perhaps I got a wrong format readcount file. Could you please upload some test readcount files?

ckockan commented 7 years ago

Can you try again with these files: https://github.com/sfu-compbio/sinvict/archive/sample-data.zip

HaoKuo commented 7 years ago

Thanks for the super fast reply, ckockan . Things went well with your readcount files. Obviously, I got a wrong format readcount file.