gforg34
commented
2 months ago Hi @weirdo-onlooker,
I am facing the same problem using SLURM, did you manage to solve the problem? "Wrote 48415 instead of 146868 objects of type ubyte to file `/tmp/sambamba-pid17362-markdup-nirv/PairedEndsInfotopn4' (No space left on device)"
and in another file with similar run this:
sambamba-markdup: Cannot open file /tmp/sambamba-pid9095-markdup-xsnx/PairedEndsInfowvtf5' in modew+' (No space left on device)
But the /tmp file seems to have more than enough available space.
I also tried this but I do not understand the actual usage of it:
Note: This command gave me the first ERROR. The second ERROR appears with neither hash-table-size nor overflow-list-size, just sambamba markdup and the files.
sambamba markdup -t 4 --hash-table-size=4194304 --overflow-list-size 1000000
by following these two threads issue177 and this issue169.
Any help would be appreciated.
@pjotrp Hello, when I was running the command
"sambamba markdup -t 1 results/GCF_030020395.1/bams/preMerge/pangolin/PNG1.bam results/GCF_030020395.1/bams/pangolin_final.bam 2 > logs/GCF_030020395.1/sambamba_dedup/pangolin.txt,"
I encountered the following error:
vbnetCopy code sambamba 0.8.0 by Artem Tarasov and Pjotr Prins (C) 2012-2020 LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
finding positions of the duplicate reads in the file... sambamba-markdup: Wrote 4089 instead of 144157 objects of type ubyte to file `/tmp/sambamba-pid21662-markdup-qkux/PairedEndsInfohgbw24' (No space left on device)
At the same time, the server administrator reminded me that the /tmp directory is full. How can I change the location where temporary files are written?