rastiks
commented
6 years ago When I set the a dir as the output I was asked for a file :
-machine:~/sbt_project_UMI$ java -jar bfx-examples/pipelines/target/scala-2.12/bfx-examples-pipelines.jar SingleStrandUmiSomaticVariantCalling --input-bam=/xdrive/umiPipeline/anntotated.bam -ref=/hg19/genome.fa --intervals=/xdrive/umiPipeline/E7000.bed --output=./test2
Exception in thread "main" java.lang.AssertionError: assertion failed: Cannot write file because it is a directory: /home/rasta/sbt_project_UMI/test2
at scala.Predef$.assert(Predef.scala:219)
at com.fulcrumgenomics.commons.io.IoUtil.assertCanWriteFile(Io.scala:119)
at com.fulcrumgenomics.commons.io.IoUtil.assertCanWriteFile$(Io.scala:115)
at com.fulcrumgenomics.commons.io.Io$.assertCanWriteFile(Io.scala:34)
at com.nilshomer.bfx.examples.pipelines.SingleStrandUmiSomaticVariantCalling.
Hi. We tryied to test the bfx-examples so far with no succes .... Could not find the way to continue ... Could you help please ? Thnx . R.
sbt test ended with success... but ...
machine:~/sbt_project_UMI$ 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)