Hi Andreas, > On Thu, Feb 28, 2019 at 10:38:52AM +0200, Graham Inggs wrote: >> Control: found -1 0.11.7+dfsg-1 >> Control: title -1 fastqc: autopkgtest regression >> Control: user -1 debian...@lists.debian.org >> Control: usertags -1 regression >> >> As per the link in the bug report, the autopkgtest failures coincided with >> the upload of 0.11.7+dfsg-1. > > Once you commited > > commit ce4840ca8ec57c52fc144eb9b5695e8f02f0f5e5 > Author: Sascha Steinbiss <sa...@debian.org> > Date: Thu Dec 8 19:04:06 2016 +0000 > > add some BAM/SAM test data > > > containing test data and commands to process these data. This is > failing since 0.11.7+dfsg-1 as Graham confirmed. Can you please > check whether there are some issues with these test data or whether > the commands have changed?
The BAM/SAM files are just the SAM example from the samtools distribution [1] and its BAM equivalent. They should be fine (in face, I picked them for being provided as examples by the authors of the file format). I can’t say whether they reflect real-life data or not as I am not too familiar with that. However, I can reproduce the issue here. Looks like a real bug introduced in 0.11.7 (or a dependency?) Not sure what you mean with ’the commands have changed’…? I get the same issue in the GUI version of FastQC, so I guess it has nothing to do with the test suite call but rather with how these files are handled internally. Cheers Sascha [1] https://raw.githubusercontent.com/samtools/samtools/develop/examples/toy.sam
