Question: "ERROR: cannot create temp file" when using buildindex from Rsubread
0
gravatar for efernandez
7 weeks ago by
efernandez0
efernandez0 wrote:

Hi everybody

I'm trying to use the buildindex function from Rsubread and the following error apears:

>buildindex(basename="./hg19.subread",reference="hg19.fa")

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 1.34.7

//================================= setting ==================================\\
||                                                                            ||
||                Index name : hg19.subread                                   ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : no                                             ||
||                                                                            ||
||       Free / total memory : 30.2GB / 31.4GB                                ||
||                                                                            ||
||               Input files : 1 file in total                                ||
||                             o hg19.fa                                      ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
ERROR: cannot create temp file

the working directory is the one were the hg19.fa file is located. Any idea?

ADD COMMENTlink modified 7 weeks ago by Gordon Smyth39k • written 7 weeks ago by efernandez0
Answer: "ERROR: cannot create temp file" when using buildindex from Rsubread
2
gravatar for Wei Shi
7 weeks ago by
Wei Shi3.2k
Australia
Wei Shi3.2k wrote:

Your working directory does not seem to be writable. buildindex needs to have write permission to the directory so it can write temporary files and output index files.

ADD COMMENTlink written 7 weeks ago by Wei Shi3.2k
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