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  • #8

Closed
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Opened Mar 07, 2023 by Yaroslav Tal@yaro.tal

Segmentation Fault on non-existing files

When a FASTA file is passed to obitools (e.g. obicount) that does not exist, the result is a hard segfault, for example:

./mosaicquastassembly/asm/assembly.fasta
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x28 pc=0x5f9168]

goroutine 1 [running]:
git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert._ExpandListOfFiles.func1({0x7ffff36cb8a0?, 0x28?}, {0x0?, 0x0?}, {0x44ecd2?, 0x640?})
        /home/yaro/obitools4.1onPkD/obitools4-master/pkg/obitools/obiconvert/sequence_reader.go:23 +0x88
path/filepath.Walk({0x7ffff36cb8a0, 0x28}, 0xc0000f3e00)
        /home/yaro/obitools4.1onPkD/go/src/path/filepath/path.go:569 +0x50
git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert._ExpandListOfFiles(0x0, {0xc000091020, 0x1, 0x64e71f?})
        /home/yaro/obitools4.1onPkD/obitools4-master/pkg/obitools/obiconvert/sequence_reader.go:20 +0xf2
git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert.CLIReadBioSequences({0xc000091020, 0x1, 0x1})
        /home/yaro/obitools4.1onPkD/obitools4-master/pkg/obitools/obiconvert/sequence_reader.go:110 +0x598
main.main()
        /home/yaro/obitools4.1onPkD/obitools4-master/cmd/obitools/obicount/main.go:36 +0x91
./mosaicquastunicycler_gapclosed_assembly/asm/unicycler_gapclosed_assembly.fasta
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x28 pc=0x5f9168]
Edited Mar 07, 2023 by Yaroslav Tal
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Reference: obitools/obitools4/obitools4#8