Does anyone have any experience running snpEff on Galaxy?
We installed snpEff from the toolshed and now have the latest
changeset (c052639fa666).
We modified the config files to correct the pathnames but now we're running
into a series of errors when we try to run '*Compute SNP effect*' with a
file using the hg19 dataset
*The first error was:*
java.lang.RuntimeException: Property: 'hg37.genome' not found
at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:78)
at
ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:334)
at ca.mcgill.mcb.pcingola.snpEffect.Config.read(Config.java:301)
at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:67)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:582)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:261)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:77
This first error was confusing because the input file was for hg19, so it's
not clear why there was a reference to hg37.
Next, we then edited snpEff.config and added the line
*hg37.genome : Homo_sapiens*
*
*
with the other hg37.XX : Homo_sapiens keypairs.
*This led to the second error:*
ERROR: Cannot read file
'/home/galaxy//snpEff/data//hg37/snpEffectPredictor.bin'.
You can try to download the database by running the following command:
java -jar snpEff.jar download hg37
java.lang.RuntimeException: java.io.FileNotFoundException:
/home/galaxy/snpEff/data/hg37/snpEffectPredictor.bin (No such file or
directory)
at
ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
at
ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:240)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:595)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:261)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:77)
Caused by: java.io.FileNotFoundException:
/home/galaxy/snpEff/data/hg37/snpEffectPredictor.bin (No such file or
directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:137)
at java.io.FileInputStream.<init>(FileInputStream.java:96)
at
ca.mcgill.mcb.pcingola.util.Gpr.readFileSerializedGzThrow(Gpr.java:468)
at
ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:55)
... 4 more
The problem now is that is is looking for the hg37 directory, which
doesn't exist but GRCh37.65 does exist. So we then change the directory
name to hg37 and reran, resulting in the third error:
VcfFileIterator.parseVcfLine(276): Fatal error reading file
'/mnt/galaxyData/files/000/dataset_432.dat' (line: 1):
1 2338204 2338204 G/T +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING:
Unkown IUB code for SNP '+'
at
ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:277)
at
ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:331)
at
ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:1)
at
ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:69)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:215)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:698)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:648)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:261)
at
ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:77)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '+'
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parseAlts(VcfEntry.java:530)
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parse(VcfEntry.java:445)
at ca.mcgill.mcb.pcingola.vcf.VcfEntry.<init>(VcfEntry.java:66)
at
ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:274)
... 8 more
I'm going to assume that this is all related to the first issue, but I'm
not sure how to fix the issue.
Cheers!
Rob
Rob Leclerc, PhD
<http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc>
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
Personal Email: rob.lecl...@aya.yale.edu
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