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

[Fleur Peters]

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. 

Best,

Fleur Peters

[Bo Li]

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?

Best,

Bo

--
RSEM website: http://deweylab.biostat.wisc.edu/rsem/
---
You received this message because you are subscribed to the Google Groups "RSEM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rsem-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/rsem-users/a4d63713-f874-4e86-acad-1ac4ee0edf0bn%40googlegroups.com.

[Fleur Peters]

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 :) 

Best,

Fleur

Op donderdag 16 september 2021 om 16:00:36 UTC+2 schreef lijig...@gmail.com: