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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Bismark installation issue? #3117

Closed naumenko-sa closed 4 years ago

naumenko-sa commented 4 years ago

Hello everyone!

I'm updating bcbio with

bcbio_nextgen.py upgrade -u skip --data --genomes BDGP6 --datatarget smallrna

And it seems that bismark does not skip reference installation (it has been installed already):

Writing bisulfite genomes out into a single MFA (multi FastA) file

Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019)

A directory called /n/shared_db/bcbio/biodata/genomes/Dmelanogaster/BDGP6/bismark/Bisulfite_Genome/ already exists. Already existing converted sequences and/or already existing Bowtie 2 or HISAT2) indices will be overwritten!

It works fine for human genome, something is wrong with non-human?

Sergey

roryk commented 4 years ago

Thanks, I can take a look-- it shouldn't be genome dependent at all. Are we sure the bismark genome was complete? It is possible files were missing and that is why it was not skipped. If you rerun now, does it skip it properly?

naumenko-sa commented 4 years ago

I re-ran several times, it reinstalls every time: (o2): /n/shared_db/bcbio/biodata/genomes/Dmelanogaster/BDGP6/bismark

roryk commented 4 years ago

Thanks! I must have messed up the memoization check, I'll fix it.

roryk commented 4 years ago

Thanks! I added in the step to check if the index is already made.

naumenko-sa commented 4 years ago

Thanks, it works!