failed my fastqc Quality Control process

Question: failed my fastqc Quality Control process

7 months ago by

modarzi • 0 wrote:

Hi, I downloaded sra_data_SRR1427482.fastq file. Now I want to check its quality via fastqc software in linux. I run fastqc command with name of file and I see below messages:

"Started analysis of sra_data_SRR1427482.fastq Approx 5% complete for sra_data_SRR1427482.fastq Approx 10% complete for sra_data_SRR1427482.fastq Approx 15% complete for sra_data_SRR1427482.fastq Approx 20% complete for sra_data_SRR1427482.fastq Approx 25% complete for sra_data_SRR1427482.fastq Approx 30% complete for sra_data_SRR1427482.fastq Approx 35% complete for sra_data_SRR1427482.fastq Approx 40% complete for sra_data_SRR1427482.fastq Approx 45% complete for sra_data_SRR1427482.fastq Approx 50% complete for sra_data_SRR1427482.fastq Approx 55% complete for sra_data_SRR1427482.fastq Approx 60% complete for sra_data_SRR1427482.fastq Approx 65% complete for sra_data_SRR1427482.fastq Approx 70% complete for sra_data_SRR1427482.fastq Approx 75% complete for sra_data_SRR1427482.fastq Approx 80% complete for sra_data_SRR1427482.fastq Approx 85% complete for sra_data_SRR1427482.fastq Approx 90% complete for sra_data_SRR1427482.fastq Approx 95% complete for sra_data_SRR1427482.fastq

Failed to process file sra_data_SRR1427482.fastq uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Ran out of data in the middle of a fastq entry. Your file is probably truncated at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:179) at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76) at java.lang.Thread.run(Thread.java:748)"

As you see, after progress above 95%, my quality process would be failed. I appreciate if any body help and share his/her experience with me. Best regards, Mohammad

rna-seq software error • 606 views

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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by modarzi • 0

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This forum is for using Galaxy https://galaxyproject.github.io/. General bioinformatics questions are better asked at https://www.biostars.org/, https://bioinformatics.stackexchange.com/, and sometimes tool/domain specific forums (google groups, etc).

That said, the error indicates that your fastq input has a format problem (truncated record). This could mean that the data from SRA/NCBI was not downloaded completely or some manipulation after corrupted the file. It will need to be corrected before using FastQC or any other analysis tool, line-command or within Galaxy.

For help with line-command usage and/or interpreting results (including those produced by Galaxy), consult the FastQC help https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

If you want to do this in Galaxy instead, get SRA data directly loaded with Download and Extract Reads in FASTA/Q format from NCBI SRA and then use FastQC. Sometimes data from this source needs to be standardized, help for that is here in our Support FAQs: https://galaxyproject.org/support/#getting-inputs-right

Galaxy tutorials: https://galaxyproject.org/learn/. Those at the top work at Galaxy Main https://usegalaxy.org. Start with the 101. The other first five cover usage basics in more detail and those are followed by example analysis tutorials.

Thanks! Jen, Galaxy team

ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

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