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Segmentation fault #4
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Hi, Thank you! |
Hi Francesca, I'm trying to run ~200k nanopore reads with average length ~6000 nucleotides to scaffold a 30MB draft genome. Unfortunately, there is no more output about the error and, because smis_shred does not produce the two artificial fastq files the rest of the pipeline complains about not having those files (see below). I also tried to run smis_shred stand-alone on mutliple files always with the same result. I thought it might be a compiler version problem but had the same problem with gcc4.2.1 (MAC), 4.4.7. and 4.9.4 (Centos6).
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Hi,
Also, if you have not done this, download and compile the version in the Sanger organization: https://github.com/wtsi-hpag/smis . We can continue the discussion here though. Thank you, |
I initially tried the version you pointed to but had the same problem. Also I couldn't add an issue on the other repo that's why I came here :) |
Hi, By the way, thanks for letting me know about the missing issues option on the organization repo, I think I fixed that. Thank you |
Hi Francesca I am working with the latest version and I am encountering the same issue. Could you please help ? My command is
Here are answers for your queries
Yes
Here are those
I could not find those files. Where can I find that? Looking forward to hear from you soon. Regard |
Trying to run the new version but get
Segmentation fault $bindir/smis_shred -rlength $fakelen -step $step -minlen $minlen $fqfile fakemates_1.fastq fakemates_2.fastq >> $outp
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