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IDBA issue 'std::logic_error' SequenceWriter::SequenceWriter() ostream is invalid

Hi, I am trying to merge paired-end illumina reads (read length: 101) .

I am using the command: fq2fa --merge --filter sample_1.fq sample_2.fq sample.fa

I am getting: terminate called after throwing an instance of 'std::logic_error' what(): SequenceWriter::SequenceWriter() ostream is invalid Aborted (core dumped)

I have done this with my previous batch of samples, and was able to merge the paired-end reads and then assembled them successfully. Since then my computer was wiped and so I have re-installed idba-master. Since re-installing, any command I use results in the same error. I even tried to re-assemble a merged paired-end fasta file from my previous sequencing batch. The same error is occurring, even though I had successfully assembled it in the past.

Can anyone please help.

Cheers, Tim

software error assembly next-gen
• 3,049 views • link
updated by lizelpotgieter • lizelpotgieter • written by timothy.ghaly • timothy.ghaly

I suppose you compiled the master branch? Do you know which version you had before? Can you try reverting some commits, or installing a previous release?

• 0 views • link
written by h.mon h.mon

1 answer

Hi Tim,

I know I am very late to the party. I had the same problem, but when I created the output folder for the merged reads to be written to everything worked just fine. I hope this helps.

L

• 0 views • link
written by lizelpotgieter • lizelpotgieter

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