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sambamba-markdup:(No space left on device) #509
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Hi @weirdo-onlooker, I am facing the same problem using SLURM, did you manage to solve the problem? and in another file with similar run this: But the /tmp file seems to have more than enough available space. |
@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?
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