rsem-calculate-expression error

[Huffyphenix]

Hello everyone, I am runing star-cufflinks-rsem to analyse my transnomic sequencing data, everything is all right until I turn to use rsem to calculate the gene expression. The RSEM gives me an error called: rsem-parse-alignments /project/huff/huff/stem_cell_differentiation/test/4.rsem.ref/RSEMref Quant.temp/Quant Quant.stat/Quant b /project rsem-parse-alignments : No such file or directory! Please check if you have compiled the associated codes by typing related "make" commands and/or made related executables ready to use. And I found that it is exactlly no tools called rsem-parse-alignments in my rsem install directory. And even though I installed it twice I didn't find it. And I wonder if your guys have met this problem? How to solve it? Any help will be gratefully appreciated. Thank u very much.

[Huffyphenix]

And this is my commands: RSEMgenomeDir="/project/huff/huff/stem_cell_differentiation/test/4.rsem.ref" rsem-calculate-expression --bam --no-bam-output --estimate-rspd --calc-ci --seed 12345 -p 8 --ci-memory 30000 --paired-end --forward-prob 0 /project/huff/huff/stem_cell_differentiation/test/2.star.result/Aligned.toTranscriptome.out.bam $RSEMgenomeDir/RSEMref Quant I confirmed that the RSEMgenomeDir is the reference genome generated by rsem-prepare-reference.

[bli25wisc]

@Huffyphenix Could you let me know how did you install RSEM? Did you type make under the RSEM directory?

[Huffyphenix]

@bli25wisc I download the latest archive available on the github website ( https://github.comdeweylab/RSEM ) and then add it to my PATH as below: wget -O RSEM.v1.2.25.tar.gz https://github.com/deweylab/RSEM/archive/v1.2.25.tar.gz cd RSEM-1.2.25/ make export PATH=/project/huff/huff/bin/software/rsem/rsem-1.2.22:$PATH ###add the path to my .profile and then source. After that, the RSEM reference files prepration was done without any error, but the error occured when I tried to run rsem-calculate-expression. Thank u for your attention!

[bli25wisc]

@Huffyphenix Why when you export PATH, the version is rsem-1.2.22?

[Huffyphenix]

@bli25wisc Oh, this is another version of RSEM, I installed it to see if I can solve the problem. But unfortunately not even though I installed it many times. So, do you have a tool called rsem-parse-alignments in your install directory?

[bli25wisc]

@Huffyphenix If you typed make, you should be able to find 'rsem-parse-alignments' in RSEM-1.2.25

[Huffyphenix]

@bli25wisc Ok, I will try it again. Thank you very much.

[gloriaccwang]

Hi, I got THE SAME Error, could you please let me know how did you fix this problem? I typed make, but there is still no 'rsem-parse-alignments' in RSEM-1.3.0

[Huffyphenix]

Hello, i's regret that I didn't fix it. But when I tried it again on another machine and it runs well. So I think maybe the problem is the server configuration error or no permission to some softwares. Hope it will help you.

[gloriaccwang]

Thank you. I tried to use samtools 1.3.1 instead of 1.3, and the problem solved.

On Sat, May 27, 2017 at 7:56 PM Hu FeiFei notifications@github.com wrote:

Hello, i's regret that I didn't fix it. But when I tried it again on another machine and it runs well. So I think maybe the problem is the server configuration error or no permission to some softwares. Hope it will help you.

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