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knights-lab / UTree

K-mer searching with trees
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Segmentation Fault on utree-search_gg #6

Open bhillmann opened 7 years ago

bhillmann commented 7 years ago

Using the most up to date utree-search_gg I receive a segmentation fault on the data from MSI. I haven't narrowed down if it is a specific read that is causing this issue or not.

utree-search_gg /panfs/roc/scratch/ben/projects/analysis_SHOGUN/data/references/rep82/utree/rep82.gg.ctr /panfs/roc/scratch/ben/projects/analysis_SHOGUN/data/mp2_gold/combined_seqs.fna /panfs/roc/scratch/ben/projects/analysis_SHOGUN/results/mp2_gold/rep82/utree_results.tsv RC
Using 32-bit counters
16777217 elements read.
Nodes in input tree: 1259261770 (PACKSIZE=32, CNTTYPE=NA, IXTYPE=uint16_t, SZ=7)
Read 1259261770 nodes.
Tree read properly.
Segmentation fault
GabeAl commented 7 years ago

Couple of things -- the way it's written in your log above is the old way. Is it possible you're using an old version by mistake? The newer version has no underscores in its name.

Also, the test file is very large (~200GB). It would be helpful to have a version that highlights the problem. One way to get at this is to take the first ~million sequences after the last sequence that failed to output properly in the .tsv file. Using this simplified subset I can hone in on the problem.

Cheers and thanks for the report! The GG version has gotten extremely little testing, so every little bit of info helps 👍

bhillmann commented 7 years ago

I verified that it is running with the new version of UTree search. The database may have been built with the older version of UTree. I'm not sure what version of UTree it was using for sure though for any steps. Any way we could incorporate a version string?