regading issue in key file

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Vishal Bhat

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Sep 1, 2021, 8:52:31 AM9/1/21
to TASSEL - Trait Analysis by Association, Evolution and Linkage

actually iam using gbsv2 pipeline and  iam in the ist step :-


/run_pipeline.pl -Xms100G -Xmx200G -fork1 -GBSSeqToTagDBPlugin -e EcoT22I -i /media/ram/288bdc2b-363d-468b-b93b-6f4202372eb7/tassel-5-standalone/fastq.gz -db /media/ram/288bdc2b-363d-468b-b93b-6f4202372eb7/output/gbsv2.db -k /media/ram/288bdc2b-363d-468b-b93b-6f4202372eb7/tassel-5-standalone/keyfile/6642NAAXX_key.txt -kmerLength 64 -minKmerL 20 -mnQS 20 -mxKmerNum 100000000 -endPlugin -runfork1

and iam returning with this error

GBSSeqToTagDBPlugin:processData - found NO files represented in key file.
Please verify your file names are formatted correctly and that your key file contains the required headers

please help me out form this issue what kind of files it requires
i had given all the path in te correct format

Dr Mathavan M

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Sep 1, 2021, 9:01:07 AM9/1/21
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can show your key file (6642NAAXX_key.txt )

Vishal Bhat

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Sep 2, 2021, 1:01:24 AM9/2/21
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this is the key file which iam using for gbs analysis

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6642NAAXX_key.txt

Alden Perkins

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Sep 7, 2021, 1:29:06 PM9/7/21
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It looks like you're passing TASSEL a file that isn't named following one of the naming conventions rather than a directory. The documentation for the -i argument says:

i <Input Directory>: Input directory containing FASTQ files in text or gzipped text. NOTE: Directory will be searched recursively and should be written WITHOUT a slash after its name. (REQUIRED)

And the documentation on the naming conventions for the fastq files says:

The file names should be represented as one of the formats below:

  • flowcell_lane_fastq.txt.gz
  • flowcell_s_lane_fastq.txt.gz
  • code_flowcell_s_lane_fastq.txt.gz

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