"ERROR: cannot create temp file" when using buildindex from Rsubread
1
0
Entering edit mode
efernandez • 0
@efernandez-22025
Last seen 23 months ago
Argentina

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 • 2.2k views
ADD COMMENT
2
Entering edit mode
Wei Shi ★ 3.6k
@wei-shi-2183
Last seen 2 days 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
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 776 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