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VarDict Java expected run time and memory

See original GitHub issue

Hi, Can you give an estimated run time for a given BAM file size for VarDictJava ? I understand this would be highly dependent on the system being run. I have a BAM file of 5GB in size. Running the command

AF_THR="0.01" # minimum allele frequency <path_to_vardict_folder>/build/install/VarDict/bin/VarDict -G /path/to/hg19.fa -f $AF_THR -N sample_name -b /path/to/my.bam -z -c 1 -S 2 -E 3 -g 4 /path/to/my.bed | VarDict/teststrandbias.R | VarDict/ -N sample_name -E -f $AF_THR

takes over 24 hours using 1 CPU with 16GB RAM. Is this within the expected range for runtime ? Java implementation was supposed to be 10 times faster than the perl implementation so I was expecting faster than 24 hours for a 5GB BAM file.

Thanks Best Regards T. Hamdi Kitapci

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Comments:12 (7 by maintainers)

github_iconTop GitHub Comments

PolinaBevadcommented, May 1, 2019

Hi Hamdi, Sorry I forgot to say that it must be not a simple variable, but enviromental variable, so you have to set it like this: export VAR_DICT_OPTS='"-Xms32g" "-Xmx900g"' instead of this VAR_DICT_OPTS='"-Xms32g" "-Xmx900g"' In second case it can be accessed only in scope of the script that you run and not other programs (gradle, JVM, etc). Please, try to use it with export command. You can also check that variable now is available in enviroment by starting this before VarDict: printenv | grep OPTS If everything is ok, you will get the line VAR_DICT_OPTS=‘“-Xms32g” “-Xmx900g”’`

PolinaBevadcommented, May 7, 2019

Hamdi, hello! Great, thank you for notifying! I will close the issue, please feel free to create new issue if you will have any other questions.

Read more comments on GitHub >

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