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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Execution failed: [Errno 2] No such file or directory #117

Open zhou-ran opened 5 years ago

zhou-ran commented 5 years ago

When i used pRSEM module for processing my data, there was every unclear bug about Execution failed: [Errno 2] No such file or directory. After i read source code, found that there was a error when pRSEM execute R script. pRSEM execute the r script by /bin/env, user should replace all '/bin/env' into '/usr/bin/env'.

pliu55 commented 5 years ago

Hi @luguodexxx,

Thanks for using pRSEM and reporting this issue. Could you please tell me your computing environment under which you were running pRSEM? Thanks.

Best, Peng

zhou-ran commented 5 years ago

Hi @pliu55 , I tested in Ubuntu and CentOs. And in pRSEM's makefile, the $UCSCEXEDIR download url was invalid.

pliu55 commented 5 years ago

Hi @luguodexxx,

Thanks for the info and thanks for pointing out the $UCSCEXEDIR url issue. I hard coded UCSC version 287 a few years ago to make sure the binary is exactly what we used for the pRSEM paper. As time passed by, UCSC has updated its software version. I will prepare a patch for it. Please let me know if you experienced any other issue with pRSEM.

Best, Peng

zhou-ran commented 5 years ago

Thanks for your quick reply!