Error: Features added out of order

[changd15]

Hi,
When I run asdpex-cli-0.2.jar, I get the following error on a few samples. I have ensured that the input files have been sorted. Any help would be greatly appreciated! Thanks!

**************[WARN] found no 'first' ASDP for region REGION160 set to region start.
[WARN] found no 'last' ASDP for region REGION160 set to region stop.
****Exception in thread "main" java.lang.IllegalArgumentException: Features added out of order: previous (TabixFeature{referenceIndex=13, start=105573251, end=105573293, featureStartFilePosition=451911835841, featureEndFilePosition=-1}) > next (TabixFeature{referenceIndex=13, start=105573221, end=105573267, featureStartFilePosition=451911836245, featureEndFilePosition=-1})
at htsjdk.tribble.index.tabix.TabixIndexCreator.addFeature(TabixIndexCreator.java:89)
at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.add(IndexingVariantContextWriter.java:170)
at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:219)
at de.charite.compbio.asdpex.cmd.AnnotatedVariantWriter.put(AnnotatedVariantWriter.java:62)
at de.charite.compbio.asdpex.cmd.AnnotateVCFCommand.writeVariants(AnnotateVCFCommand.java:320)
at de.charite.compbio.asdpex.cmd.AnnotateVCFCommand.run(AnnotateVCFCommand.java:292)
at de.charite.compbio.asdpex.App.main(App.java:58)
make: *** [sortvcf] Error 1

[pnrobinson]

Can you provide a little more context? Can you provide the command-line arguments you used that led to this error? Peter Robinson Professor of Computational Biology The Jackson Laboratory for Genomic Medicine 10 Discovery Drive Farmington, CT 06032 860.837.2095 t | 860.990.3130 m peter.robinson@jax.org<mailto:peter.robinson@jax.org> www.jax.org Robinson lab: https://robinsongroup.github.io/ The Jackson Laboratory: Leading the search for tomorrow's cures

…

________________________________ From: changd15 <notifications@github.com> Sent: Friday, May 19, 2017 7:30 PM To: charite/asdpex Cc: Subscribed Subject: [charite/asdpex] Error: Features added out of order (#11) Hi, When I run asdpex-cli-0.2.jar, I get the following error on a few samples. I have ensured that the input files have been sorted. Any help would be greatly appreciated! Thanks! **************[WARN] found no 'first' ASDP for region REGION160 set to region start. [WARN] found no 'last' ASDP for region REGION160 set to region stop. ****Exception in thread "main" java.lang.IllegalArgumentException: Features added out of order: previous (TabixFeature{referenceIndex=13, start=105573251, end=105573293, featureStartFilePosition=451911835841, featureEndFilePosition=-1}) > next (TabixFeature{referenceIndex=13, start=105573221, end=105573267, featureStartFilePosition=451911836245, featureEndFilePosition=-1}) at htsjdk.tribble.index.tabix.TabixIndexCreator.addFeature(TabixIndexCreator.java:89) at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.add(IndexingVariantContextWriter.java:170) at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:219) at de.charite.compbio.asdpex.cmd.AnnotatedVariantWriter.put(AnnotatedVariantWriter.java:62) at de.charite.compbio.asdpex.cmd.AnnotateVCFCommand.writeVariants(AnnotateVCFCommand.java:320) at de.charite.compbio.asdpex.cmd.AnnotateVCFCommand.run(AnnotateVCFCommand.java:292) at de.charite.compbio.asdpex.App.main(App.java:58) make: *** [sortvcf] Error 1 - You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#11>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AEtuPEyXi475VFDmJ1p7815N5-2bPw0Hks5r7iYDgaJpZM4NhHLl>. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

[changd15]

Sure thing. I have vcfs for several samples and am trying to run the ASDP extraction algorithm on them. The ASDP extraction ran successfully for a majority of the samples, but failed with above error for a few of them. I ran the following command:
java -jar target/asdpex-cli-0.2.jar annotate -a allASDPs.SNV.50_10.valid.sorted.vcf.gz -d ${asdpdir}/data/ -v vcfs/${sample}_sorted.vcf.gz -o asdpex/${sample}_sorted.asdp.vcf.gz -s ${asdpdir}/asdpex.sqlite