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I'm running MuTect as such:
java -Xmx16g -Djava.io.tmpdir=/scratch/MuTect/23/ -jar muTect-1.1.4.jar --analysis_type MuTect --dbsnp dbsnp_137.hg19.vcf --cosmic hg19_cosmic_v54_120711.vcf --input_file:normal Normal.bam --input_file:tumor Tumor.bam --reference_sequence ucsc.hg19.fasta --out out/23.txt --vcf out/23.vcf --enable_extended_output -nt 14 > out/logs/23.log
I'm having trouble with this command freezing after about 7 hours of running time. Looking at 'top', the threads are still running, but there is no more output (including in the log files). In trying to find out a cause (and that it isn't something in my local environment), I noticed that there was a huge number of temporary files:
> find /scratch/MuTect/23/ -type f -name "org*.tmp" | wc -l 348444 > du -h /scratch/MuTect/23/ 2.7G /scratch/MuTect/23/
That seems like a huge number of files to be worrying about for a single pair of samples! The command does not always freeze; other samples have processed successfully.
Here's the end of the log:
> tail out/logs/23.log INFO 18:18:45,701 MuTect - [MUTECTOR] Processed -853994073 reads in 681 ms INFO 18:18:46,335 MuTect - [MUTECTOR] Processed -852994071 reads in 634 ms INFO 18:18:46,967 MuTect - [MUTECTOR] Processed -851993833 reads in 632 ms INFO 18:18:47,603 MuTect - [MUTECTOR] Processed -850993125 reads in 635 ms INFO 18:18:48,233 MuTect - [MUTECTOR] Inspected 4345000 potential candidates INFO 18:18:48,249 MuTect - [MUTECTOR] Processed -849992893 reads in 647 ms INFO 18:18:49,233 MuTect - [MUTECTOR] Processed -847992889 reads in 0 ms INFO 18:18:49,233 MuTect - [MUTECTOR] Processed -848992891 reads in 984 ms INFO 18:18:50,742 MuTect - [MUTECTOR] Processed -846992738 reads in 1509 ms INFO 18:19:10,796 ProgressMeter - chrY:52600941 3.11e+09 8.0 h 9.3 s 98.5% 8.1 h 7.5 m