When processing them with the ngi_pipeline I get a failure for the two samples which end with PCR-free whereas the samples ending with Nano have no trouble; thus I suspect the hyphen is causing the regex to fail.
The traceback:
[2014-09-05 09:49] INFO: ngi_pipeline.piper_ngi: Building Piper setup.xml file for project "ND-0522" sample "NA10860_PCR-free", libprep "A", seqrun "140821_D00458_0029_AC45JGANXX"
[2014-09-05 09:49] INFO: ngi_pipeline.piper_ngi: Executing command line: setupFileCreator --output /proj/a2010002/nobackup/NGI/analysis_ready/ANALYSIS/ND-0522/ND-0522-NA10860_PCR-free-140821_D00458_0029_AC45JGANXX_setup.xml --project_name ND-0522 --sequencing_platform Illumina --sequencing_center NGI --uppnex_project
_id a2010002 --reference /proj/a2009002/piper_references/gatk_bundle/2.8/b37/human_g1k_v37.fasta --input_fastq /proj/a2010002/nobackup/NGI/analysis_ready/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L001_R1_001.fastq.gz --input_fastq /proj/a2010002/nobackup/NGI/analysis_ready
/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L001_R2_001.fastq.gz --input_fastq /proj/a2010002/nobackup/NGI/analysis_ready/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L002_R1_001.fastq.gz --input_fastq /proj/a2010002/nobackup/NGI/anal
ysis_ready/DATA/ND-0522/NA10860_PCR-free/A/140821_D00458_0029_AC45JGANXX/NA10860_PCR-free_ATCACG_L002_R2_001.fastq.gz
Exception in thread "main" java.lang.IllegalArgumentException: requirement failed: Just one sample hit should be possible for regexp, found: 0
at scala.Predef$.require(Predef.scala:233)
at molmed.apps.Sthlm2UUSNP$.parseSampleInfoFromFileHierarchy(Sthlm2UUSNP.scala:172)
at molmed.apps.setupcreator.SetupUtils$.molmed$apps$setupcreator$SetupUtils$$parseInfoFromFile$1(SetupUtils.scala:310)
at molmed.apps.setupcreator.SetupUtils$$anonfun$5.apply(SetupUtils.scala:314)
at molmed.apps.setupcreator.SetupUtils$$anonfun$5.apply(SetupUtils.scala:314)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.immutable.Set$Set4.foreach(Set.scala:137)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
at scala.collection.AbstractSet.scala$collection$SetLike$$super$map(Set.scala:47)
at scala.collection.SetLike$class.map(SetLike.scala:93)
at scala.collection.AbstractSet.map(Set.scala:47)
at molmed.apps.setupcreator.SetupUtils$.createXMLFromIGNHierarchy(SetupUtils.scala:314)
at molmed.apps.setupcreator.SetupFileCreator$.createSetupFile(SetupFileCreator.scala:92)
at molmed.apps.setupcreator.SetupFileCreator$$anonfun$10.apply(SetupFileCreator.scala:65)
at molmed.apps.setupcreator.SetupFileCreator$$anonfun$10.apply(SetupFileCreator.scala:58)
at scala.Option.map(Option.scala:145)
at molmed.apps.setupcreator.SetupFileCreator$delayedInit$body.apply(SetupFileCreator.scala:58)
at scala.Function0$class.apply$mcV$sp(Function0.scala:40)
at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
at scala.App$$anonfun$main$1.apply(App.scala:71)
at scala.App$$anonfun$main$1.apply(App.scala:71)
at scala.collection.immutable.List.foreach(List.scala:318)
at scala.collection.generic.TraversableForwarder$class.foreach(TraversableForwarder.scala:32)
at scala.App$class.main(App.scala:71)
at molmed.apps.setupcreator.SetupFileCreator$.main(SetupFileCreator.scala:13)
at molmed.apps.setupcreator.SetupFileCreator.main(SetupFileCreator.scala)
I've got four samples:
When processing them with the ngi_pipeline I get a failure for the two samples which end with
PCR-free
whereas the samples ending withNano
have no trouble; thus I suspect the hyphen is causing the regex to fail.The traceback:
The directory tree: