Open JoshuaDanielRubin opened 2 years ago
haansi
commented
2 years ago Sorry for the delay, was offline the last days. If you want to use the rsrs - then you need to specify the former tree phylotree17 - as the latest tree by Duer et al is provided for rCRS only.
the parameter to add --phylotree 17
JoshuaDanielRubin
commented
2 years ago Ah, I see. Thanks!
N-atalia
commented
1 year ago Sorry for the delay, was offline the last days. If you want to use the rsrs - then you need to specify the former tree phylotree17 - as the latest tree by Duer et al is provided for rCRS only.
the parameter to add --phylotree 17
Hi! is this still the case? cheers
seppinho
commented
1 year ago yes
I would like to use HaploGrep to classify a FASTA sample with respect to the RSRS, but the option does not seem to work. I get the error:
`[classify, --in, simulations/Q1.fa, --out, here, --format, fasta, --rsrs] phylotree17_FU1_rsrs.xml Parameters: Input format: fasta Phylotree version: 17_FU1 Reference: RSRS Extended report: false Skip alignment rules: false Used metric: kulczynski Chip array data: false Lineage: 0
Start Classification... [M::bwa_idx_load_from_disk] read 0 ALT contigs java.io.FileNotFoundException: phylotree17_FU1_rsrs.xml (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) at java.base/java.io.FileInputStream.open(FileInputStream.java:213) at java.base/java.io.FileInputStream.(FileInputStream.java:155)
at phylotree.PhylotreeManager.getPhylotree(PhylotreeManager.java:53)
at genepi.haplogrep.util.HgClassifier.run(HgClassifier.java:25)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:178)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:20)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine.execute(CommandLine.java:2078)
at genepi.App.main(App.java:59)
java.net.MalformedURLException
at java.base/java.net.URL.(URL.java:702)
at java.base/java.net.URL.(URL.java:564)
at java.base/java.net.URL.(URL.java:511)
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:649)
at java.xml/com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:150)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:860)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:824)
at java.xml/com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
at java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1216)
at java.xml/com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:635)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:489)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:807)
at phylotree.Phylotree.(Phylotree.java:60)
at phylotree.PhylotreeManager.getPhylotree(PhylotreeManager.java:60)
at genepi.haplogrep.util.HgClassifier.run(HgClassifier.java:25)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:178)
at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:20)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine.execute(CommandLine.java:2078)
at genepi.App.main(App.java:59)
Caused by: java.lang.NullPointerException
at java.base/java.net.URL.(URL.java:608)
... 24 more
`
However the program works without the --rsrs flag.