Closed komalsrathi closed 7 years ago
Hi @komalsrathi , have you compiled RSEM v1.2.25? Here is the usage information I extracted from the error report above for RSEM v1.2.25:
Usage: rsem-extract-reference-transcripts refName quiet gtfF sources hasMappingFile [mappingFile] chromosome_file_1 [chromosome_file_2 ...]
Note that it contains an additional argument "sources" between "gtfF" and "hasMappingFile". "sources" was added in later versions of RSEM but not v1.2.25.
What I suspect is that you installed a later version globally and you might forget to compile RSEM v1.2.25 by typing 'make'. Thus, RSEM uses 'rsem-extract-reference-transcripts' from the later version.
Hope it helps, Bo
Thanks! I will give that a try!
There may have been compiling problems but I just used the conda version and it works.
Hello,
I am trying the same command with two different versions and don't understand what's going wrong:
This is with version: RSEM v1.2.31
This is with an older version 1.2.25 which I need to replicate this pipeline: