Closed 0xaf1f closed 7 years ago
When running the commands under the section "Prediction" at http://kplogo.wi.mit.edu/manual.html#examples, I get a segmentation fault after the second command.
I've tried this on CentOS 6 and from within a Debian 9 container with the same results. This is with the latest release 1.0.
$ kpLogo gRNA.txt -weighted -o model_training [Tue Jul 18 17:15:22 2017] Summary: [Tue Jul 18 17:15:22 2017] Input : gRNA.txt [Tue Jul 18 17:15:22 2017] Background : local [Tue Jul 18 17:15:22 2017] Output : model_training.* [Tue Jul 18 17:15:22 2017] alphabet : ACGT [Tue Jul 18 17:15:22 2017] min_kmer : 1 [Tue Jul 18 17:15:22 2017] max_kmer : 4 [Tue Jul 18 17:15:22 2017] min_shift : 0 [Tue Jul 18 17:15:22 2017] max_shift : 0 [Tue Jul 18 17:15:22 2017] p : 1.010000 [Tue Jul 18 17:15:22 2017] start at : 1 [Tue Jul 18 17:15:22 2017] 1841 sequences loaded from gRNA.txt [Tue Jul 18 17:15:22 2017] making frequency logo... [Tue Jul 18 17:15:22 2017] making information content logo... [Tue Jul 18 17:15:22 2017] fixed position: 25 26 [Tue Jul 18 17:15:22 2017] fixed residual : G G [Tue Jul 18 17:15:22 2017] 340 exact kmers to be tested [Tue Jul 18 17:15:22 2017] 9288 tests (kmer x position x shifts) will be performed [Tue Jul 18 17:15:23 2017] 5941 positional kmers with p <1.010000 [Tue Jul 18 17:15:24 2017] plotting the most significant kmer at each position... G G [Tue Jul 18 17:15:24 2017] plotting single nucleotide profile... [Tue Jul 18 17:15:27 2017] Done! $ kpLogo gRNA.txt -predict model_training [Tue Jul 18 17:15:31 2017] Summary: [Tue Jul 18 17:15:31 2017] Input : gRNA.txt [Tue Jul 18 17:15:31 2017] Background : local [Tue Jul 18 17:15:31 2017] Output : kpLogo.* [Tue Jul 18 17:15:31 2017] alphabet : ACGT [Tue Jul 18 17:15:31 2017] min_kmer : 1 [Tue Jul 18 17:15:31 2017] max_kmer : 4 [Tue Jul 18 17:15:31 2017] min_shift : 0 [Tue Jul 18 17:15:31 2017] max_shift : 0 [Tue Jul 18 17:15:31 2017] p : 1.010000 [Tue Jul 18 17:15:31 2017] start at : 1 [Tue Jul 18 17:15:31 2017] 1841 sequences loaded from gRNA.txt [Tue Jul 18 17:15:31 2017] making frequency logo... [Tue Jul 18 17:15:32 2017] making information content logo... [Tue Jul 18 17:15:32 2017] fixed position: 25 26 [Tue Jul 18 17:15:32 2017] fixed residual : G G [Tue Jul 18 17:15:32 2017] === prediction mode === [Tue Jul 18 17:15:32 2017] building model from file: model_training.pass.p.cutoff.txt [Tue Jul 18 17:15:32 2017] - 5719 positional kmers included in the model [Tue Jul 18 17:15:32 2017] scoring input sequences using the model... [Tue Jul 18 17:15:33 2017] - done Segmentation fault
I've identified bugs that could potentially cause this error. Please try the updated version from the master branch.
Alright, I don't see the segfault anymore. Thanks for tagging a new release!
When running the commands under the section "Prediction" at http://kplogo.wi.mit.edu/manual.html#examples, I get a segmentation fault after the second command.
I've tried this on CentOS 6 and from within a Debian 9 container with the same results. This is with the latest release 1.0.