awk + samtools sort step was really slow

[苏茜薇]

hello, the awk + samtools sort step runs over 3 days for a 700G sam file, which I think is abnormal. Firstly when I used juicer to do the alignment, it successfully generated the sam file(~700G), and it errored as "samtools sort failed, too many files open", then I add "-m 3G" to the samtools sort command in juicer.sh to decrease to number of files increased, and rerun with "-S chimeric", it didn't give out the same error "samtools sort failed, too many files open ", and started to run normally. I wait it for 3 days, It was still running, and created many bam temp files, I'm not sure if I should continue wait, or can you give some suggestions about the situation? 

I installed the juicer following the mannual in wiki, "git clone https://github.com/theaidenlab/juicer.git 

cd <myJuicerDir> 

ln -s ~/juicer/CPU scripts cd scripts/common 

wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar ln -s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar 

cd ../.."

hope to get your response.

Qianwei

[Moshe Olshansky]

Hi Qianwei,

How many threads are you using? Check when the last temporary bam file was created. If it happened recently then the process is running and I would wait.

Good luck,

Moshe.