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hartwigmedical / hmftools

Various algorithms for analysing genomics data
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java.nio.file.NoSuchFileException: /workspace/purple/circos/COLO829T.circos.conf #364

Closed bobrad98 closed 1 year ago

bobrad98 commented 1 year ago

Hi,

I'm trying to run PURPLE 3.7.2 with the test data that you provided:

java -jar purple_v3.7.2.jar 
-reference COLO829R 
-tumor COLO829T 
-output_dir /workspace/purple 
-amber /project-files/AMBER 
-cobalt /project-files/COBALT 
-gc_profile /project-files/ref_hg37/GC_profile.1000bp.37.cnp 
-ref_genome /project-files/ref_hg37/HMFtools-Resources_ref_genome_37_Homo_sapiens.GRCh37.GATK.illumina.fasta 
-ref_genome_version 37 
-ensembl_data_dir /project-files/ref_hg37/ensembl_37

and I get this error:

java.nio.file.NoSuchFileException: /workspace/purple/circos/COLO829T.circos.conf at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:219) at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:478) at java.base/java.nio.file.Files.newOutputStream(Files.java:220) at java.base/java.nio.file.Files.write(Files.java:3425) at com.hartwig.hmftools.purple.plot.CircosCharts.writeConfig(CircosCharts.java:172) at com.hartwig.hmftools.purple.plot.CircosCharts.writeConfig(CircosCharts.java:151) at com.hartwig.hmftools.purple.plot.CircosCharts.write(CircosCharts.java:75) at com.hartwig.hmftools.purple.plot.Charts.write(Charts.java:54) at com.hartwig.hmftools.purple.PurpleApplication.performFit(PurpleApplication.java:435) at com.hartwig.hmftools.purple.PurpleApplication.processSample(PurpleApplication.java:236) at com.hartwig.hmftools.purple.PurpleApplication.run(PurpleApplication.java:174) at com.hartwig.hmftools.purple.PurpleApplication.main(PurpleApplication.java:654)

It seems to me that PURPLE didn't generate /output_dir/circos and Java gets confused. I tried to make that subdirectory manually, before running the tool, and the tool worked perfectly.

Can you help me figure out what I'm doing wrong? Thanks!

charlesshale commented 1 year ago

Could you re-try this but set the circos in path, eg: -circos /path_to_circos/

Purple creates the output directories it needs. In your example the plots should be created here: /workspace/purple/COLO829T/plot/