roryk
commented
4 years ago I think when you installed the STAR genome for mm10, the first time it failed, the STAR directory looks incomplete. If you remove /proj/conlonlb/bcbio/genomes/Mmusculus/mm10/star and redo bcbio_nextgen.py upgrade -u skip --genomes mm10 --aligners star it will regenerate it. You'll need 40G or so for the job for it to not fail though.
drlaurenwasson
Hello,
I am trying to use bcbio-nextgen to align to mm10 using STAR and I get this error:
Aligning lane C57_adult_heart with star aligner [2020-06-27T11:50Z] Running 1st pass of STAR aligner on /proj/conlonlb/users/wasson/C57-female-1-resub-2_001_R1.fastq.gz and /proj/conlonlb/bcbio/genomes/Mmusculus/mm10/star/ [2020-06-27T11:50Z] EXITING because of FATAL ERROR: could not open genome file /proj/conlonlb/bcbio/genomes/Mmusculus/mm10/star//genomeParameters.txt [2020-06-27T11:50Z] SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions [2020-06-27T11:50Z] Jun 27 07:50:20 ...... FATAL ERROR, exiting
when I head over to /proj/conlonlb/bcbio/genomes/Mmusculus/mm10/star I have the following files in there:
Therefore I concluded that something must have happened in the upgrade to STAR. So I tried to upgrade bcbio_nextgen.py upgrade -u skip --genomes mm10 --aligners star
and it tells me it's complete outfile: Upgrading bcbio-nextgen data files List of genomes to get (from the config file at '{'genomes': [{'dbkey': 'mm10', 'name': 'Mouse (mm10)', 'indexes': ['seq', 'twobit'], 'annotations': ['problem_regions', 'dbsnp', 'vcfanno', 'transcripts', 'rmsk', 'mirbase']}], 'genome_indexes': ['star', 'rtg', 'bwa', 'hisat2'], 'install_liftover': False, 'install_uniref': False}'): Mouse (mm10) Preparing STAR index from /proj/conlonlb/bcbio/genomes/Mmusculus/mm10/seq/mm10.fa. bcbio-nextgen data upgrade complete.
How do I get this file? Thanks Lauren