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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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Error when input *fq and *fa files simultaneously. #56

Closed zhouqiansolab closed 5 years ago

zhouqiansolab commented 5 years ago

The wtdbg can accept files in fa or fq format and allows multiple files following the -i. But when I input files in different format, like -i s1.fa.gz -i s2.fq.gz , the program ended with "core dump" at the "loading reads" stage. Can wtdbg support the fa and fq files in the same run?

ruanjue commented 5 years ago

Please test whether the bug came from gz, or mixture of fasta and fastq. It will be kind to offer me a small test data to reproduce the bug.

Jue

zhouqiansolab commented 5 years ago

In my test, -i s1.fasta.gz -i s2.fastq.gz and -i s1.fasta -i s2.fastq both ended with "core dump", only -i s1.fasta -i s2.fasta worked.

ruanjue commented 5 years ago

Thanks for the information. I will test mixture seq formats.

ruanjue commented 5 years ago

I found the problem, but it looks hard to fix it. I will state it in https://github.com/ruanjue/wtdbg2#limitations .

Thanks for the BUG report.

zhouqiansolab commented 5 years ago

Thanks for the reply. I think it is not a big problem and users can easily avoid it by choosing proper input files.

在 2019年1月11日，下午3:02，Jue Ruan notifications@github.com 写道：

I found the problem, but it looks hard to fix it. I will state it in https://github.com/ruanjue/wtdbg2#limitations https://github.com/ruanjue/wtdbg2#limitations .

Thanks for the BUG report.

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