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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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ERROR in temp file #114

Open robertosirica opened 3 years ago

robertosirica commented 3 years ago

Hello, I' m currently performing a variant calling on human fastq with LoFreq, I'm experimentig the issue in the title, and the following error appears: ERROR(lofreq_call.c|main_call:1408): Couldn't open /tmp/lofreq2-call-dyn-bonf.m6pt5o ERROR(lofreq_call.c|main_call:1408): Couldn't open /tmp/lofreq2-call-dyn-bonf.Q3JZXo ERROR(lofreq_call.c|main_call:1408): Couldn't open /tmp/lofreq2-call-dyn-bonf.8NdFDn ERROR(lofreq_call.c|main_call:1408): Couldn't open /tmp/lofreq2-call-dyn-bonf.JjJTbv

This error shows up only for some samples of the same run, for other samples the software works perfectly, could you help me in some way? Best Regards

andreas-wilm commented 3 years ago

Hi Roberto,

this is indeed a bit weird. Which version are you using? This happens before LoFreq does anything at all. If you are running this on a cluster, could it be that this happens on one specific node and that something's wrong there with /tmp? You could also try to write to /tmp before you're running LoFreq (e.g. touch a file there), just to see if everything's okay with /tmp.

Andreas