"ERROR: cannot create temp file" when using buildindex from Rsubread
1
0
Entering edit mode
efernandez • 0
@efernandez-22025
Last seen 22 months ago

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?

software error Rsubread buildindex • 379 views
ADD COMMENT
2
Entering edit mode
Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 20 hours ago
Australia/Melbourne/Olivia Newton-John …

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 COMMENT

Login before adding your answer.

Traffic: 996 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6