Error when converting SAM to TOPM using TASSEL 5.2.18

[Arthur Porto]

Hi,

I have a small SAM file  that I want to convert to TOPM (see file attached). However, every time I try to convert it using TASSEL, i get the following error:

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.18  Date: December 10, 2015

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 10670 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_20

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 7

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8

[Thread-5] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.FileLoadPlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.SAMConverterPlugin: time: Dec 17, 2015 16:01:47

[Thread-6] INFO net.maizegenetics.plugindef.AbstractPlugin - 

SAMConverterPlugin Parameters

i: C:\Users\Arthur\momDom9.sam

o: C:\Users\Arthur\9.topm.bin

l: 2

t: false

Reading SAM format tag alignment from: C:\Users\Arthur\momDom9.sam

Found 3393 tags in SAM file.  Assuming BWA file format.

Catch in reading SAM alignment file at tag 0:

length=64count=1 16 9 5954 1 64M * 0 0 GTTTGTATGATCAGTTATAATTACAGCCGTGCTTCTACTACTGCCTCTTCCAGTTCTAGCTGCA ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:43T20 YT:Z:UU

Error: java.lang.NullPointerException

java.lang.NullPointerException

at net.maizegenetics.dna.map.TagsOnPhysicalMap.parseSAMAlignment(TagsOnPhysicalMap.java:597)

at net.maizegenetics.dna.map.TagsOnPhysicalMap.readSAMFile(TagsOnPhysicalMap.java:531)

at net.maizegenetics.analysis.gbs.SAMConverterPlugin.processData(SAMConverterPlugin.java:69)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

Any idea of what the error might be?

Thanks,

Arthur

[Arthur Porto]

Not really. I just started from scratch and things ended up working, I think it was related to the way the chromosomes were named in the sam file.

On Thu, Sep 15, 2016 at 5:23 PM, GPetersen <gertje_...@gmx.de> wrote:

Hi Arthur,

Di you ever solve this problem? - I get the same error messages...

Thanks,

Gertje

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[Jeff Glaubitz]

My best guess is that TagsOnPhysicalMap.parseSAMAlignment expects an “X0” field to be present in BWA format SAM files, where 0 = zero.  Arthur seemed to have a “XO” field instead (where O = capital o).

Best,

Jeff

length=64count=116 95954 164M *0 0GTTTGTATGATCAGTTATAATTACAGCCGTGCTTCTACTACTGCCTCTTCCAGTTCTAGCTGCAffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffAS:i:-6 XS:i:-6XN:i:0 XM:i:1XO:i:0 XG:i:0NM:i:1 MD:Z:43T20YT:Z:UU

Error: java.lang.NullPointerException

java.lang.NullPointerException

at net.maizegenetics.dna.map.TagsOnPhysicalMap.parseSAMAlignment(TagsOnPhysicalMap.java:597)

at net.maizegenetics.dna.map.TagsOnPhysicalMap.readSAMFile(TagsOnPhysicalMap.java:531)

at net.maizegenetics.analysis.gbs.SAMConverterPlugin.processData(SAMConverterPlugin.java:69)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

Any idea of what the error might be?

Thanks,

Arthur

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