Question: snpsift filter fatal error
gravatar for sara.mehrabi
17 months ago by
sara.mehrabi40 wrote:

Hi all, I want to use SnpSift Filter, but each time an error occurred. any idea? thanks in advance. /Sara

Fatal error: Exit code 255 (Error) line 2:0 token recognition error at: '"' java.lang.RuntimeException: java.lang.RuntimeException: LexerNoViableAltException('"') at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory.compile( at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdFilter.parseExpression( at at at at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main( Caused by: java.lang.RuntimeException: LexerNoViableAltException('"') at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory$1.recover( at org.antlr.v4.runtime.Lexer.nextToken( at org.antlr.v4.runtime.BufferedTokenStream.fetch( at org.antlr.v4.runtime.BufferedTokenStream.sync( at org.antlr.v4.runtime.BufferedTokenStream.setup( at org.antlr.v4.runtime.BufferedTokenStream.lazyInit( at org.antlr.v4.runtime.CommonTokenStream.LT( at org.antlr.v4.runtime.Parser.enterRule( at ca.mcgill.mcb.pcingola.snpSift.antlr.SnpSiftParser.compilationUnit( at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory.compile( ... 5 more Caused by: LexerNoViableAltException('"') at org.antlr.v4.runtime.atn.LexerATNSimulator.failOrAccept( at org.antlr.v4.runtime.atn.LexerATNSimulator.execATN( at org.antlr.v4.runtime.atn.LexerATNSimulator.match( at org.antlr.v4.runtime.Lexer.nextToken( ... 13 more SnpSift filter -f /home/galaxy/galaxy/database/files/000/dataset_292.dat -e /home/galaxy/galaxy/database/jobs_directory/000/317/tmpbw3hhh SnpSift version 4.1l (build 2015-10-03), by Pablo Cingolani

Usage: java -jar SnpSift.jar filter [options] 'expression' [input.vcf] Options: -a|--addFilter <str> : Add a string to FILTER VCF field if 'expression' is true. Default: '' (none) -e|--exprFile <file> : Read expression from a file -f|--file <input.vcf> : VCF input file. Default: STDIN -i|--filterId <str> : ID for this filter (##FILTER tag in header and FILTER VCF field). Default: 'SnpSift' -n|--inverse : Inverse. Show lines that do not match filter expression -p|--pass : Use 'PASS' field instead of filtering out VCF entries -r|--rmFilter <str> : Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field). Default: '' (none) -s|--set <file> : Create a SET using 'file' --errMissing : Error is a field is missing. Default: false --format <format> : SnpEff format version: {2, 3}. Default: Auto --galaxy : Used from Galaxy (expressions have been sanitized).

snp • 735 views
ADD COMMENTlink written 17 months ago by sara.mehrabi40
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Sara, This is difficult for me to diagnose (although we may still get more input from the IUC developers).

What we will need to know: The job was run on a local, correct? Has the tool worked in the past on other datasets? If not, do other tools from this tool suite work? Is your local at the latest Galaxy release 17.05 and is the latest tool version 4.1.1 installed? Do you use conda dependency resolution?

Or, if you able to reproduce the problem at, would you please send in a bug report for this error? We can then help to determine if the problem is with the inputs, settings, or with the tool itself. The tool was last updated some time ago - before the most recent methods for dependency resolution were fully integrated into Galaxy.

Or, you can share the settings (contents of the "i" job details page) and some lines of the input dataset(s) (header plus 100 or so lines of data) and we can try to determine the problem from there. When sharing data of this size, a link would be good. This can be a gist or to dropbox folder/file or any web source that is publically accessible. We might need to rerun to fully test.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k

Hi Jennifer,

here are the answers,

I run the job on local, just because the tool (snpsift) was not available on Galaxy server as a result I can not send the bug from usegalaxy. the tool snpeff was working and used to produce the vcf file. we have the latest version of both galaxy and tool. as far as I understood the latest version of galaxy install conda as default.

here is the vcf file here is the link to (i)

Thanks, /Sara

ADD REPLYlink modified 17 months ago • written 17 months ago by sara.mehrabi40

Sorry, I forgot this tool wasn't installed at

Update: The server is hosted publically. It might be quicker for me to review the history that contains the job (I can see all the data from the view details page, but just stats). A history share link can be generated and sent to This is a private email internal to the core Galaxy team and your data would not be shared publically. Include a link to this post so we can associate the two.

ADD REPLYlink modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson25k

Also, it looks like you removed a comment about reruns with the smaller and larger version of the file. The error could indicate a format problem and/or the tool running out of memory. This type of error is not always trapped. If you are an admin at your instance, the memory issue could be checked. Or, you could contact the admin to see if they can help. Let us know.

ADD REPLYlink written 17 months ago by Jennifer Hillman Jackson25k

Hi Jennifer,

Thanks for your reply, Yes I remove the comments, because I thought my comment will make every thing more complicated. as you saw in my comment I got result once and with out changing any thing I got error afterward. because of some unknown reason for me, it start to work after I tried for several times and got failed. any way I run this step. thanks again. I would like to know about snpsift filters, there are some example there, but is there any link with more options/suggestions for filters?

thanks a lot /Sara

ADD REPLYlink written 17 months ago by sara.mehrabi40

Sara, very glad the tool is working now! For more examples of the Filter tool's syntax, please see the manual, specifically here:

If the filter syntax is entered in an unexpected format that too can cause a confusing warning, output, and/or errors. With this and other tools with free-form parameter entry, within Galaxy or not. Once you learn the syntax rules, this will almost certainly get easier.

Take care, Jen

ADD REPLYlink written 17 months ago by Jennifer Hillman Jackson25k
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