time for generating human genome with annotations

[Tiffany Ting Liu]

I was wondering how long it takes to index the human genome with annotations? It's been running for ~1.5 days. I used a single thread. Would this be correct? Thank you so much.

Best,

Tiffany

[Alexander Dobin]

Hi Tiffany,

this seems too long. Even with one thread it should take only a few hours. Please send me your Log.out file.

Cheers

Alex

[Andy Teich]

Hi - was this issue ever resolved?  I am having the exact same problem.  I can also send my Log.out file if that would help.  Thank you for any input/advice.

Andy

[Alexander Dobin]

Hi Andy,

I am not sure it's the same issue, but I have fixed a bug in 2.5.0a/b that was causing stalling of genome generation in some cases.

Please check the latest patch on GitHub master.

Cheers

Alex

[steve Shen]

Dear Alex,

It seems to be similar situation for me that process is stalling when generating reference with annotation file. We are using precompiled STAR in Linux_x86_64_static folder of 2.5.0b (downloaded today).

The genome sequence is Homo_sapiens.GRCh38.dna.chromosome.5.fa and GTF file is Homo_sapiens.GRCh38.82-Chr5.gtf, which only chr5 entries are used from general GTF file. Thanks in advance for advice.

By the way, many thanks for this wonderful software. We have been using STAR for DNA variation and RNA splicing detection recently.

Regards,

Steve

[Alexander Dobin]

Hi Steve,

could you please send me the Log.out file from the stalled run?

Cheers

Alex