rsem-calculate-expression error message

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Yvonne Zhao

Jun 1, 2022, 3:48:07 AM6/1/22
to RSEM Users

I've been trying to follow the tutorial with the data provided. I managed to prepared reference sequence but am stuck with the rsem-calculate-expression step:

Below is my command in Mac terminal: 

rsem-calculate-expression -p 1 \

            --paired-end \

            --bowtie2 \

            --bowtie2-path /Users/yvonnezhao/miniconda/bin \

            --estimate-rspd \

             --append-names \

             --output-genome-bam \

/Users/yvonnezhao/RSEM_tutorial/data/SRR937564_1.fastq \

/Users/yvonnezhao/RSEM_tutorial/data/SRR937564_2.fastq \

/Users/yvonnezhao/RSEM_tutorial/ref/mouse_ref  \


It first proceeds but then stopped with the error message:

[E::hts_open_format] Failed to open file "b" : No such file or directory

Assertion failed: (in != 0), function BamWriter, file ./BamWriter.h, line 54.

"rsem-run-em /Users/yvonnezhao/RSEM_tutorial/ref/mouse_ref 3 exp/LPS_6h exp/LPS_6h.temp/LPS_6h exp/LPS_6h.stat/LPS_6h -p 1 -b b exp/LPS_6h.temp/LPS_6h.bam 0 --append-names" failed! Plase check if you provide correct parameters/options for the pipeline!

Could you help me understand which part went wrong and how to fix it? 

Ruban Rex Peter

Jun 22, 2022, 11:36:51 AM6/22/22
to RSEM Users
Were you able to fix this error?

Yvonne Zhao

Jun 22, 2022, 2:40:48 PM6/22/22
Yes, I did! It worked out when I replace the RSEM package included in the tutorial package with an updated RSEM package. 

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