Data failed to pass FastQC (but previous pass before): Likely truncated input file

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Hello,

I trying to do a QC for my files. And I keep encountering this error. This data set had previously pass the FastQC without any error before. However, when re-upload the file to do some re-analysis, now it keeps failing to pass QC. Anyone encounters the same problem and know how to solve it?

“Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/040/717/40717303/_job_tmp -Xmx7g -Xms256m
Failed to process file AG10_Phi_DeltaLL_S8_L001_R1_001_fastq_gz.gz
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.base/java.lang.Thread.run(Thread.java:834)
cp: can’t stat ‘/corral4/main/jobs/040/717/40717303/working/dataset_53bb4f0c-c6c8-45b3-a706-13605487098b_files/*/fastqc_data.txt’: No such file or directory”

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Hi @Vu_Ngo – Check the size of your dataset as the error message indicates the data is truncated. That could have occurred during the re-upload, or maybe it wasn’t fully downloaded originally.

If the data is intact wherever you downloaded it, you probably just need to load it again. And if it is large or you are working on a slower connection, try using FTP upload as that tool will report a partial upload (plus you can resume the transfer).

I added some tags to your post that point to prior Q&A about how to do this.

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@jennaj Thanks you so much; following your comments, I was able to fix the problem :slight_smile:

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