New Member with Trimmomatic questions

[juliannf]

Hello, I would like to start off by saying hello to all and thank you so much for providing such indepth support. I have done some scouring on this site and am impressed with some of the resolutions members are able to provide.

That being said I am trying to us trimmomatic 0.36 to trim the output from the first step in the CROPS pipeline. I am doing this instead of using the CROPS script itself because I am using Platform LSF and trimmomatic 0.36 is available.

Trimmomatic is telling me "Sequence and quality length don't match". I am not sure what would be causing this as I am using unmodified files from step 1 of CROPS.

This is the .err file I am getting from the mainframe and wonder if anyone has an idea on what the issue could be?

Picked up _JAVA_OPTIONS: -Xmx512m
TrimmomaticSE: Started with arguments:
-phred33 /nethome/j.fiorentino3/GBS_Data/HFM7HBBXX/parsed/HFM7HBBXXCTGC_001.R1parsed.fastq.gz /nethome/j.fiorentino3/GBS_Data/HFM7HBBXX/parsed/HFM7HBBXXCTGC.trimmed.fq.gz ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
Automatically using 1 threads
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Exception in thread "main" java.lang.RuntimeException: Sequence and quality length don't match: 'AATGGAGGGTGCTCAGCAAACACATAAACACACAACCATGTCCCATCAGCCTCCTGGAATGGTAGTGATCTAGATTATTGTGAGACAAAG' vs 'JJAFJFJJFJFFJJFJJJJFJFJJ77FAFJJFJJJJJFFJA<<FJA<FA-AF7FAFJJJAFJJAAJJF<AJJ7A'
at org.usadellab.trimmomatic.fastq.FastqRecord.<init>(FastqRecord.java:25)
at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:89)
at org.usadellab.trimmomatic.fastq.FastqParser.next(FastqParser.java:179)
at org.usadellab.trimmomatic.TrimmomaticSE.processSingleThreaded(TrimmomaticSE.java:60)
at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:222)
at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

[GenoMax]

You appear to have one read (at least) where the sequence length does not match the quality score line length (corrupt fastg record). You can do something like

 $ grep -A 3 "AATGGAGGGTGCTCAGCAAACACATAAACACACAACCATGTCCCATCAGCCTCCTGGAATGGTAGTGATCTAGATTATTGTG" your_file

and examine that record for corruption.

[tmhpxk6]

Hi,

In line with questions by new users of Trimmomatic, I was wondering what "Using Long Clipping Sequence" means? Appreciate help in understanding this.