rsem-calculate-expression with STAR takes forever but without error

Hi all,

I am running rsem-calculate-expression after succesfully generating the reference files with rsem-prepare-reference. However, the command never proceeds past: “started mapping” like in the example below

Sep 16 08:44:43 ….. started STAR run

Sep 16 08:44:43 ….. loading genome

Sep 16 08:44:46 ….. started mapping

The code that I’m using is this:

rsem-calculate-expression -p 14 --paired-end --star HNLMFDSXY_104305-001-002_CGATGCTT-CGTAGATG_L003_R1.fastq HNLMFDSXY_104305-001-002_CGATGCTT-CGTAGATG_L003_R3.fastq ref/human_ensembl results/CD4_CLL2

I’ve let it run for days on end but it doesn’t finish, any clue on what it going wrong or how to troubleshoot? Since I don’t get an error either, it’s a bit a mystery what is going on.

I’m using a SSH with 16 cores and 64 GB RAM and the sample is paired-end with ~20M reads.

Thanks a lot for any help or suggestions.

Best,
Fleur Peters