Error with sv_prep

[insilicool]

Hi,

I am testing sv_prep for potential addition to our workflow, but unfortunately, it is erroring out when parsing the known_fusion_data.37.csv from the latest resource bundle

Error: 15:40:46.242 [main] [INFO ] SvPrep version: 1.0.1 15:40:46.262 [main] [INFO ] refGenome(V37), bam(alignment/COLO829T/COLO829T.sorted.dup.recal.bam) 15:40:46.263 [main] [INFO ] output(SVariants/COLO829/GRIDSS/sv_prep/) 15:40:46.306 [main] [ERROR] invalid hotspot entry: Type,FiveGene,ThreeGene,CancerTypes,PubMedId,KnownExonTranscript,KnownExonUpRange,KnownExonDownRange,HighImpactPromiscuous,Overrides 15:40:46.359 [main] [INFO ] loaded 6402 blacklist locations from file

Command:

module purge && module load mugqic/java/openjdk-jdk-19 && \ mkdir -p SVariants/COLO829/GRIDSS/sv_prep && \ java -XX:+UseParallelGC -XX:ParallelGCThreads=1 -Dsamjdk.buffer_size=4194304 -Xmx36G \ -jar bin/sv-prep_v1.0.1.jar -threads 6 \ -sample COLO829T \ -bam_file alignment/COLO829T/COLO829T.sorted.dup.recal.bam \ -ref_genome Homo_sapiens.hs37d5.fa \ -ref_genome_version 37 \ -blacklist_bed hmf_pipeline_resources.37_v5.31/sv/sv_prep_blacklist.37.bed \ -known_fusion_bed hmf_pipeline_resources.37_v5.31/sv/known_fusion_data.37.csv \ -output_dir SVariants/COLO829/GRIDSS/sv_prep

Also, I've added -log_debug and -log_level DEBUG to the argument and it outputs the same uninformative error.

Any help would be much appreciated.

Thanks, Rob Eveleigh

[p-priestley]

I think you parsed the wrong file into the algorithm. You need to use this file: known_fusions.37.bedpe (not the csv file)

[insilicool]

Apologizes. Indeed that was the issue.

Unfortunately, a new issue has arisen when applying the algorithm to the reference using the tumor junctions.

Command: module purge && module load mugqic/java/openjdk-jdk-19 && \ java -XX:+UseParallelGC -XX:ParallelGCThreads=1 -Dsamjdk.buffer_size=4194304 -Xmx36G \ -jar bin/sv-prep_v1.0.1.jar -threads 6 \ -sample COLO829N \ -bam_file COLO829N.sorted.dup.recal.bam \ -ref_genome Homo_sapiens.hs37d5.fa \ -ref_genome_version 37 \ -blacklist_bed hg37.blacklist.bed \ -known_fusion_bed known_fusions.37.bedpe \ -existing_junction_file SVariants/COLO829/GRIDSS/sv_prep/COLO829T.sv_prep.junctions.csv \ -output_dir SVariants/GRIDSS/COLO829/sv_prep

Error: 08:21:07.360 [main] [INFO ] SvPrep version: 1.0.1 08:21:07.370 [main] [INFO ] refGenome(V37), bam(alignment/COLO829N/COLO829N.sorted.dup.recal.bam) 08:21:07.371 [main] [INFO ] output(SVariants/GRIDSS/COLO829/sv_prep/) 08:21:07.380 [main] [INFO ] loaded 458 known hotspot records from file 08:21:07.381 [main] [INFO ] loaded 164 blacklist locations from file 08:21:07.387 [main] [ERROR] failed to create junction writer: java.io.FileNotFoundException: SVariants/GRIDSS/COLO829/sv_prep/COLO829N.sv_prep.junctions.csv (No such file or directory) Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Error opening file: file:///lb/project/mugqic/projects/DREAM_techdev/SVariants/GRIDSS/COLO829/sv_prep/COLO829N.sv_prep.bam at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:306) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:276) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:252) at com.hartwig.hmftools.svprep.BamWriter.initialise(BamWriter.java:44) at com.hartwig.hmftools.svprep.BamWriter.(BamWriter.java:30) at com.hartwig.hmftools.svprep.ResultsWriter.(ResultsWriter.java:64) at com.hartwig.hmftools.svprep.SvPrepApplication.(SvPrepApplication.java:30) at com.hartwig.hmftools.svprep.SvPrepApplication.main(SvPrepApplication.java:133) Caused by: java.nio.file.NoSuchFileException: SVariants/GRIDSS/COLO829/sv_prep/COLO829N.sv_prep.bam at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:218) at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:484) at java.base/java.nio.file.Files.newOutputStream(Files.java:228) at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:294) ... 7 more

Best, Rob E.

[charlesshale]

Hi Rob,

SvPrep doesn't currently create new output directories, so it will need the one you specify to exist:

-output_dir SVariants/GRIDSS/COLO829/sv_prep

Can you try that?

thanks,

Charles