error with setupBarcodeFiles: java.lang.ArrayIndexOutofBoundsException:0

[shilai zhang]

Hi,

I have run different versions tassel -from tassel 3 to tassel 5. I want to use the GBS pipeline, but i have not done it successfully and it always shows that “error with setupBarcodeFiles: java.lang.ArrayIndexOutofBoundsException:0” when I run the first step - fastqtotagcount

anyone who can help me?

Many thanks!!!!

shilai

[Lynn Carol Johnson]

Shilai -

Please send us specifics on how you’ve run the command, including debug information as shown here:

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf?rev=a3538d6b2542f93a0daf108b9631e341158cf33e

Thanks - Lynn

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[张石来]

Hi Lynn,

I command is as below,

run_pipeline.bat -fork1 -FastqToTagCountPlugin -i C:\data\GBS1\fastq -k C:\data\GBS1\key.txt -e PstI-MspI -o C:\data\GBS1\tagCounts -endPlugin -runfork1

and the log is attached.

thanks!

Shilai

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[Lynn Carol Johnson]

Hi Shilai -

Will you send me the headers and first few lines of your key file?  Also, if this isn’t tassel 5, can you send me a TASSEL 5 log and add “-debug” to the command line?

Thanks - Lynn

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[Lynn Carol Johnson]

Also, there is a new tassel 5 build out (yesterday).  Please run with that – thanks!

[张石来]

Hi Lynn，

The key file is attached. And the command i send to you yesterday is  run by TASSEL 5.

I will try the new version tassel 5 later.

Thanks!

Shilai

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[Lynn Carol Johnson]

Shilai – 

Your key file (key.txt) has 100 lines, but only the first 4 have actual data.  The other lines appear to be blank lines with tabs.  The software reads these lines and tries to parse them, resulting in the ArrayOutOfBounds error.  Try truncating the file to get rid of these extra lines.

Thanks - Lynn

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[张石来]

Hi Lynn,

Thank you very much! Yes, I clear up the blank lines for the key file. And it works now!

Thanks again. You solve my hard trouble.

Shilai

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