Failed at align step - Githubissues

EichlerLab / smrtsv2

Structural variant caller

MIT License

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Failed at align step #13

Closed bioysu closed 5 years ago

bioysu commented 5 years ago

I tried to run smrtsv2 with PacBio reads from yeast following tutorial: /pfs1/liuguanghui/suyao/tools/smrtsv2/smrtsv index /pfs1/liuguanghui/suyao/data/UCSC/sacCer3/chromosomes/sacCer3.fa /pfs1/liuguanghui/suyao/tools/smrtsv2/smrtsv align /pfs1/liuguanghui/suyao/tools/smrtsv2/test_yeast2/reads2.fofn here is the output: default here is the log file in align/bam/log default

Could you tell me how to fix the problem?

RSherman15 commented 5 years ago

I had this problem as well; see issue #6. Downgrading hdf5 in the pacbio conda environment to 1.10.3 to 1.10.2 fixed it.

paudano commented 5 years ago

Thanks @RSherman15. The build system in dep now installs this version as well. You might have cloned the repository before that change was pushed. You might want to pull changes and rebuild dep (make clean and make).

I am closing for now, but let me know if this doesn't fix the problem.

bioysu commented 5 years ago

The align step is OK now.