nh13 / bfx-examples

Bioinformatics Example Repository

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bfx-examples's Issues

Exception in thread "main" com.fulcrumgenomics.sopt.cmdline.ValidationException

Hi. We tryied to test the bfx-examples so far with no succes .... Could not find the way to continue ... Could you help please ? Thnx . R.

sbt test ended with success... but ...

machine:~/sbt_project_UMI$ java -jar bfx-examples/pipelines/target/scala-2.12/bfx-examples-pipelines.jar SingleStrandUmiSomaticVariantCalling --input-bam=/xdrive/umiPipeline/S29.bam -ref=/hg19/genome.fa --intervals=/xdrive/umiPipeline/E7000.bed --output=./test2.txt

[2018/07/31 11:32:51 | DagrCoreMain | Info] SingleStrandUmiSomaticVariantCalling failed. Elapsed time: 0.02 minutes.
Exception in thread "main" com.fulcrumgenomics.sopt.cmdline.ValidationException
at dagr.core.cmdline.DagrCoreArgs.configure(DagrCoreMain.scala:142)
at dagr.core.cmdline.DagrCoreMain.makeItSo(DagrCoreMain.scala:234)
at dagr.core.cmdline.DagrCoreMain.makeItSoAndExit(DagrCoreMain.scala:213)
at dagr.core.cmdline.DagrCoreMain$.main(DagrCoreMain.scala:55)
at dagr.core.cmdline.DagrCoreMain.main(DagrCoreMain.scala)

CONFIG FILE :
###############################################################################

DAGR configuration file

################################################################################

Some basic dagr configuration

dagr = {
command-line-name = "bfx-examples-pipeline"
path = ${PATH} // tell dagr to search for executables using the system path by default
package-list = ["com.nilshomer.bfx.examples"]
}

Config variables that are used to set other paths

pipeline_dir = /home/sbt_project_UMI/bfx-examples/pipeline/bin

Task Configuration

picard.jar = ${pipeline_dir}/picard.jar
fgbio.jar = ${pipeline_dir}/fgbio.jar
bwa.executable = ${pipeline_dir}/bwa
bwa-kit.dir = ${pipeline_dir}/bwa.kit
vardictjava.dir = ${pipeline_dir}/VarDictJava
bfx-examples-tools.jar = ${pipeline_dir}/bfx-examples-tools.jar

FYI :
/home/sbt_project_UMI/bfx-examples/pipeline/bin contains all the binary files (bwa, picard, fgbio, bfx-examples-tools) + directory bwa. kit with binaries + directory VarDictJava with binaries (VarDict-1.5.4.jar)