Question: FASTQC issue getting error in web page
0
gravatar for rgambhir
3.0 years ago by
rgambhir10
United States
rgambhir10 wrote:

Thank you for that. I did finally upload my sequence using the file zilla. First I changed my .gz file into fastq using the gunzip command on the terminal. then uploaded this file using the ftp (filezilla). I was trying to do some FastQC on it and i could see my data on the RAW page but was unable to see in the web page format. Please let me know what should do in this regard. Also, I am trying to develop a pipeline for DNA-Seq analysis. so the plan is to do FastQC and align the data against the latest human genome build up.

Regards

Ratish

 

Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch Failed to process file EL2_RG14_032315_R2_001.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Ran out of data in the middle of a fastq entry. 

error upload format fastqc fastq • 2.4k views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson24k • written 3.0 years ago by rgambhir10
1
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

This error indicates that the fastq file is malformed. It could be that it was truncated in the middle of the upload or that it is truncated before upload.(due to some upstream problem).

Start by checking the FTP load - Filezilla will report if a transfer is complete or not as a status (see the bottom tabs in that tools interface). If a transfer was interrupted, it can be resumed by logging into Galaxy again and moving the file over. 

If the transfer was complete, then check the fastq file. On your computer, examine the last few lines. In Galaxy, do the same (the line tools in "Text Manipulation" can help). 

Also, with an error in Galaxy, clicking on the bug report will provide more information with certain tools. Fastq Groomer is one that will tell you exactly where the first occurrence of a problem sequence is located. 

More troubleshooting help:
http://wiki.galaxyproject.org/Support#Error_from_tools

Best, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson24k
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