-
Notifications
You must be signed in to change notification settings - Fork 2
Open
Description
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!
Reactions are currently unavailable
Metadata
Metadata
Assignees
Labels
No labels