search

rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
547 stars 131 forks source link

unicycler crashes during hybrid assembly #150

Open silargi opened 5 years ago

silargi commented 5 years ago

Hello, Unicycler has been repeatedly crashing while running a hybrid assembly with Illumina reads + GridIon long reads. The error is (in more than 3 attempts): /software/pathogen/internal/prod/bin/unicycler: line 6: 17324 Illegal instruction /software/pathogen/external/apps/usr/local/Python-3.6.0/bin//unicycler ${@:1} This seems to happen at this step: Aligning long reads to graph using minimap

Except for one run when the error was: Error: SPAdes crashed!

I've discuss this issue with a few people and the current belief is that this issue is caused by a bug in unicycler.

Some additional information: I've used unicycler successfully many times on this cluster for hybrid assembly (illumina+pacbio or illumina+minion)], and it hasn't been updated since. Unicycler ran ok with example data provided. Canu v 1.7 has assembled the long reads ok. The GridIon data runs fine through Porechop, but the same error is encountered regardless.

Let me know if you need any further details/files. Thank you!

caspargross commented 5 years ago

Might be related to issue #153 Downgrading to version 0.4.4 fixes this problem.

Your SPAdes crash is unrelated.