rsem-calculate-expression running time endless but also no error

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Fleur Peters

Sep 16, 2021, 6:50:27 AM9/16/21
to RSEM Users
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. 

Thanks a lot for any help or suggestions. 

Fleur Peters

Bo Li

Sep 16, 2021, 10:00:36 AM9/16/21
Hi Fleur,

This is definitely weird. It seems the STAR aligner is halting. Can you try to align your reads using STAR first and see if you can finish?


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Fleur Peters

Sep 21, 2021, 5:40:51 AM9/21/21
to RSEM Users
Hi Bo,

Thanks for your reply. Indeed separately doing the alignment and then using the aligned.toTranscriptome.bam as input into rsem-calculate-expression worked. So not sure what it was but anyway, it works :) 


Op donderdag 16 september 2021 om 16:00:36 UTC+2 schreef
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