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seqan / flexbar

flexible barcode and adapter removal
BSD 3-Clause "New" or "Revised" License
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Abort when running flexbar -n option #13

Closed mariehoffmann closed 6 years ago

mariehoffmann commented 6 years ago

I get a Killed: 9 error msg after a couple of minutes when running flexbar -r $dir/1-1A_S11_L001_R1_001.fastq -a $dir/1-1A_S11_L001_I1_001.fa -n 8 The index file is about 1.5 MB, the read file 15.6 MB. I use the latest flexbar version built locally on MacOS Sierra (10.12.6). I installed the tbb (version 2018_U2) via port, and build with cmake version 3.8.2, MacPorts gcc7 7.2.0_0. Running without the -n option takes very long. I will give an update, if flexbar will terminate without error.

For a better user experience, it would be good to incorporate the tbb CMakeLists.txt from e.g. https://github.com/justusc/FindTBB or print at least a warning when the TBB_FOUND flag is false.

Also, when giving a fastq file as adapter/index file instead of a fasta file, the error msg is just: Could not open with no hint. It took me a while to figure out that only fasta format is here allowed.

mariehoffmann commented 6 years ago

The Killed: 9 issue is related to index file size. As a preprocessing I reduced the index file size to unique sequences (50 lines now) and it works now as expected!