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Question: fatal error exit code 1 from Trimmomatic when input fastq data has an incorrect datatype assignment
1
gravatar for chrisscotland
2.6 years ago by
chrisscotland • 10
chrisscotland • 10 wrote:

trying to run my dataset with trimmomatic

I have changed the files to fast-q-sanger, but it isn't recognising the format so I cant run as group set, and when I run as a single it fails with the fatal error exit code 1

please help
fastq upload fastqsanger.gz datatype fastqsanger • 2.0k views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by chrisscotland • 10
1
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The datatype is fastqsanger. Make sure all inputs have this assigned. It is required for both single and paired-end data. At least one dataset has this assigned correctly. Test if the reads really are in fastqsanger format with FastQC (Sanger Fastq +33, aka Illumina 1.8+), and based on those results, either use the FastqGrommer or directly assign the datatype fastqsanger. This should resolve the problem.

Details covered in the Galaxy Support FAQs: https://galaxyproject.org/support/

Note: Starting with the latest Galaxy releases:

  1. Uncompressed fastq reads that are already in fastqsanger format will have that datatype automatically assigned by the Upload tool when the datatype is "autodetected".
  2. Compressed fastq reads (.gz), that you wish to remain uncompressed once the history, need to be assigned the datatype fastqsanger.gz when loading through the Upload tool.
  3. When "autodetect" is used when loading compressed fastq reads, these will be uncompressed, checked to see if in fastqsanger format, and loaded into the history with the fastqsanger datatype assigned if the fastq reads are a match for that datatype specification.*

Thanks! Jen, Galaxy team

admin edit: updated links and added notes about the Upload tool's datatype autodetection function.
ADD COMMENT • link modified 7 months ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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