This is a test version of Biostars. For the public version, visit https://www.biostars.org.
bbduk truncated fastq file according to FastQC - help?

I was able to succeessfully remove adapters from my PE 150bp x 2 reads using bbduk.sh, but I kept seeing that I had a long string of Gs in my R2 sequences (~ 0.1% of my R2 reads).

I reran the original fastq files with bbduk to remove the string of Gs, and this worked for most of my PE files except for one pair.

When I ran this trimmed set of PE reads through FastQC (after bbduk), I received an error that said:

Failed to process file EA_Pool-POW_1-1a_S28_L001_R1_CLEANEST.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:77)
    at java.lang.Thread.run(Thread.java:722)

Has anyone encountered this issue before with output fastqs from bbduk?

Should I just not worry about the ~0.1% of GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG kmers in my R2 reads?

Thank you!

bbduk metagenome pe fastqc
• 2,931 views • link
updated by swbarnes2 swbarnes2 • written by lintonf • lintonf

1 answer

I'd start by rerunning the trimming; it might have just randomly stopped.

Honestly, a string of G's isn't going to align to anything, so it's not going to do anything bad if you leave them in.

• 0 views • link
written by swbarnes2 swbarnes2

That was my thought, and it's such a low % of the R2 reads. Thanks for the input!

• 0 views • link
written by lintonf • lintonf

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.

Upvote|Bookmark|Accept

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this
  • error in Fastq
    written by lonekaisar72 • lonekaisar72
    HI I am trying to do fastqc of one file but after running approximately 100 percent it is showing the below-listed error Please suggest what …
  • Fastqc genome reads
    written by Ak • Ak
    Hi! I'm trying to check the quality of my raw genome reads using fastqc, but I'm encountering this issue. Does anyone what can I do …
  • FastQC error (failure to process fastq.gz file)
    written by mdmoandd • mdmoandd
    I was wondering why I got this error when using fastqc. Do I need to unzip my fastq.gz file first maybe? Started analysis of 16_2.fastq.gz …
  • assembly of fastq_pair results (4 files )
    written by Bioinfo • Bioinfo
    Hello everyone I have two files containing reads that I want to assembly I run spades and it shows this error message Error log: == …
  • Failure in generating fastq from human fasta
    written by marongiu.luigi marongiu.luigi
    Hello, I have created some mutated human sequences modifying the GCRh38 fasta files. I then concatenated the files adn generated the fastq files with $ …
  • How to repair corrupted fastq files after sortmeRNA
    written by SMILE SMILE
    Hi all, After removing rRNA in the fastq files with sortmeRNA, one of the paied reads was corrupetd, which failed to do fastqc with error: …
  • tophat equal length problem
    written by HK • HK
    Hey, I am running an RNA seq pipeline, all my samples gave the output after mapping except one and it gives an error: prep_reads v2.1.1 …
  • tophat equal length problem
    written by HK • HK
    Hey, I am running an RNA seq pipeline, all my samples gave the output after mapping except one and it gives an error: prep_reads v2.1.1 …
  • RNA-seq fastqc error
    written by zz105 • zz105
    I'm running fastqc on command line, and one of the files gives me a error: sun-java version jdk1.7.0_02 loaded fastqc version 0.10.1 loaded Started analysis …
  • fastq file error
    written by Pals Pals
    Hi, After removing rRNAs using sortmerna, 2/42 files failed fastqc with error: > uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't > start with '@' at > uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158) > …