Entering edit mode
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?
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?
Please make sure that the current running directory is writable and it has sufficient space (like >=4GBytes for building a human index).
Ok, but how can I check if the current directory is writable? :)
You can try this:
But given that you have created two sub-directories under the current directory, it seems to be writable. Can you also try this:
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.