Error in "igvtools count"

[Sowmya]

igvtools count throws an error while accessing a resource from igvdata for mm10. This was working as of last month.

We use IGV tools version "IGV Version EA (2)04/09/2013 11:51 AM"

Here is the stack trace:

ERROR [2017-09-12 06:33:50,624]  [ParsingUtils.java:156] [main]  Error getting content length for: http://igvdata.broadinstitute.org/genomes/seq/mm10/chr1.fa
java.io.FileNotFoundException: File not found: http://igvdata.broadinstitute.org/genomes/seq/mm10/chr1.fa
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:561)
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:481)
at org.broad.igv.util.HttpUtils.getHeaderField(HttpUtils.java:212)
at org.broad.igv.util.HttpUtils.getContentLength(HttpUtils.java:219)
at org.broad.igv.util.ParsingUtils.getContentLength(ParsingUtils.java:140)
at org.broad.igv.feature.genome.FastaIndexedSequence.<init>(FastaIndexedSequence.java:41)
at org.broad.igv.feature.genome.FastaDirectorySequence.readIndexes(FastaDirectorySequence.java:38)
at org.broad.igv.feature.genome.FastaDirectorySequence.<init>(FastaDirectorySequence.java:31)
at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:286)
at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:124)
at org.broad.igv.tools.IgvTools.loadGenome(IgvTools.java:981)
at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:696)
at org.broad.igv.tools.IgvTools.run(IgvTools.java:311)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:197)
org.broad.igv.tools.PreprocessingException: Unexpected IO error: 
at org.broad.igv.tools.IgvTools.run(IgvTools.java:409)
at org.broad.igv.tools.IgvTools.main(IgvTools.java:197)
Caused by: java.io.FileNotFoundException: File not found: http://igvdata.broadinstitute.org/genomes/seq/mm10/chr1.fa.fai
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:561)
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:481)
at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:477)
at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:185)
at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:179)
at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:105)
at org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:73)
at org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:55)
at org.broad.igv.feature.genome.FastaIndex.parseIndexFile(FastaIndex.java:79)
at org.broad.igv.feature.genome.FastaIndex.<init>(FastaIndex.java:46)
at org.broad.igv.feature.genome.FastaIndexedSequence.<init>(FastaIndexedSequence.java:45)
at org.broad.igv.feature.genome.FastaDirectorySequence.readIndexes(FastaDirectorySequence.java:38)
at org.broad.igv.feature.genome.FastaDirectorySequence.<init>(FastaDirectorySequence.java:31)
at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:286)
at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:124)
at org.broad.igv.tools.IgvTools.loadGenome(IgvTools.java:981)
at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:696)
at org.broad.igv.tools.IgvTools.run(IgvTools.java:311)

[James Robinson]

Hi,  you will need to update your version of igvtools.  The version you are running is 4 years old and no longer supported,  the file it is referencing has been replaced. 

Alternatively you can hack around this by doing the following  (1) with IGV shutdown open your  igv/genomes folder and remove mm10.genome.    (2) Start IGV and load the mm10.genome.    (3) shutdown igv again,  there should be an updated mm10.genome file in igv/genomes.   Copy this file to the genomes folder of your igvtools directory.

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