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Error in FASTQ, record 0, with these 4 lines: (missing plus) #9

@schorlton-bugseq

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@schorlton-bugseq

Thanks for the great tools! I'm hitting an odd error:

fasterq-dump SRR12695179

micromamba install -y bbmap -c conda-forge -c bioconda -c defaults

bbduk.sh in=SRR12695179.fastq outm=fail.fastq entropy=0.55
java -ea  --add-modules jdk.incubator.vector -Xmx293m -Xms293m -cp /opt/conda/opt/bbmap-39.76-0/bbtools.jar bbduk.BBDukS in=SRR12695179.fastq outm=fail.fastq entropy=0.55
WARNING: Using incubator modules: jdk.incubator.vector
Executing bbduk.BBDukS [in=SRR12695179.fastq, outm=fail.fastq, entropy=0.55]
Version 39.76

Allocating kmer table:  Initial:
Memory: max=308m, total=308m, free=266m, used=42m

Input is being processed as unpaired
Exception in thread "FastqStreamer-Worker-1" java.lang.AssertionError: 
Error in SRR12695179.fastq, record 0, with these 4 lines: (missing plus)
@SRR12695179.1 1 length=113
GAGGTGGCAGTGAAGCCAGTTATTGGAATACCGGAAATAGATTGGTAAAGGTGTGGGGCGTTTTTACGGACTACCGTGTGACTTATACGCAACAGCGATATGTAGATGCTATT
+SRR12695179.1 1 length=113
8<4/2'&#$$%676@GC8J9?**-?C/&56C=7@8?<=A:0/1(:6=G2.383$(,2*011>=74&&.0+%%%2;9:3-98001489%%7,'6666;9@<9;;02157<=-,)

        at stream.FASTQ.quadToReadVec(FASTQ.java:895)
        at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:393)
        at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:320)
        at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:193)

Of note, downgrading to v39.15 installed via bioconda does not encounter this error. Thanks again!

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