"ERROR: cannot create temp file" when using buildindex from Rsubread
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efernandez • 0
@efernandez-22025
Last seen 2.1 years 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 • 702 views
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Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 19 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.

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Hi, I ran the command : subread-buildindex -o referrence/GRCh38.fa.Subread_index -F -M 8000 GRCh38.primary_assembly.genome.fa > logs/genomeindex.Subread.log 2>&1 and had the same error. How can I solve it?

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Please make sure that the current running directory is writable and it has sufficient space (like >=4GBytes for building a human index).

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Ok, but how can I check if the current directory is writable? :)

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You can try this:

touch test.txt ; ls -l test.txt

But given that you have created two sub-directories under the current directory, it seems to be writable. Can you also try this:

df -h

to see what is the "Avail" space in the disk column of your current directory? Sorry that I don't know which volume it is, but if you see some volumns to have a 100% Use, it may suggest that the disk is full.

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