STAR for mapping RNA-Seq data to hg38

[kimal999]

Hi,

Can we map RNA-Seq data to hg38 with STAR? I have tried both stable and development versions. STAR directory is empty for both of the versions.

Version info

• bcbio version (bcbio_nextgen.py --version): 1.25
• OS name and version (lsb_release -ds):Red Hat Enterprise Linux Server release 7.4 (Maipo)

To Reproduce Exact bcbio command you have used:

bcbio_nextgen.py upgrade --genomes hg38 --aligners star --cores 16

Your sample configuration file:

Observed behavior Error message or bcbio output:

Expected behavior A clear and concise description of what you expected to happen.

Log files Please attach (10MB max): bcbio-nextgen.log, bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log.

Additional context Add any other context about the problem here.

[roryk]

Hi @kimal999,

Hm-- this should work, we strip off the ALT and patches from the hg38 build so STAR will work with it. What was the output of the command you ran? Could you try adding the -u skip and --data options to the command you ran?

[kimal999]

Hi @roryk ,

Thank you very much for the response.

Exact bcbio command

bcbio_nextgen.py upgrade --genomes hg38 --aligners star --cores 16 -u skip --data

Output

Upgrading bcbio
Upgrading bcbio-nextgen data files
--2021-02-02 10:37:48--  https://github.com/chapmanb/cloudbiolinux/archive/master.tar.gz
Resolving github.com (github.com)... 140.82.112.3
Connecting to github.com (github.com)|140.82.112.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/master [following]
--2021-02-02 10:37:48--  https://codeload.github.com/chapmanb/cloudbiolinux/tar.gz/master
Resolving codeload.github.com (codeload.github.com)... 140.82.114.10
Connecting to codeload.github.com (codeload.github.com)|140.82.114.10|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘STDOUT’

     0K ........ ........ ........ ........ ........ ........ 2.31M
  3072K ........ ........ ........ .......                    1.73M=2.4s

2021-02-02 10:37:51 (2.04 MB/s) - written to stdout [5191731]

List of genomes to get (from the config file at '{'genomes': [{'dbkey': 'hg38', 'name': 'Human (hg38) full', 'indexes': ['seq', 'twobit', 'bwa', 'hisat2'], 'annotations': ['ccds', 'capture_regions', 'coverage', 'prioritize', 'dbsnp', 'hapmap_snps', '1000g_omni_snps', 'ACMG56_genes', '1000g_snps', 'mills_indels', '1000g_indels', 'clinvar', 'qsignature', 'genesplicer', 'effects_transcripts', 'varpon', 'vcfanno', 'viral', 'purecn_mappability', 'simple_repeat', 'af_only_gnomad', 'transcripts', 'RADAR', 'rmsk', 'salmon-decoys', 'fusion-blacklist', 'mirbase'], 'validation': ['giab-NA12878', 'giab-NA24385', 'giab-NA24631', 'platinum-genome-NA12878', 'giab-NA12878-remap', 'giab-NA12878-crossmap', 'dream-syn4-crossmap', 'dream-syn3-crossmap', 'giab-NA12878-NA24385-somatic', 'giab-NA24143', 'giab-NA24149', 'giab-NA24694', 'giab-NA24695']}], 'genome_indexes': ['star', 'bwa', 'rtg', 'hisat2'], 'install_liftover': False, 'install_uniref': False}'): Human (hg38) full
hg38 detected, building a simple reference with no alts, decoys or HLA from bcbio/genomes/Hsapiens/hg38/seq/hg38.fa to bcbio/genomes/Hsapiens/hg38/seq/hg38-simple.fa.
Preparing STAR index from bcbio/genomes/Hsapiens/hg38/seq/hg38-simple.fa.
Removing bcbio/genomes/Hsapiens/hg38/seq/hg38-simple.fa.
bcbio-nextgen data upgrade complete.
Upgrade completed successfully.

Still the STAR directory is empty.

[roryk]

Hi @kimal999,

Does bcbio/genomes/Hsapiens/hg38/star exist? If you delete it and rerun does it actually build the index?

[roryk]

bcbio should be checking in your-genome-path/genomes/Hsapiens/hg38/star, is there a partially created STAR directory there?

[kimal999]

Hi @roryk,

I'm very sorry for the late reply. I think it's a problem with the memory. I was able to generate the index outside of bcbio.

Thanks again for the help.