Trimmomatic Failure

trimmomatic
fastqsangergz
fastqgz

#1

I have 12 paired end RNAseq samples, 11 of them were properly processed by Trimmomatic with no issues but one dataset fails with the following error details (see below), any advice what might be wrong?

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/022/068/22068712/_job_tmp -Xmx7g -Xms256m
TrimmomaticPE: Started with arguments:
-threads 1 -phred33 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/cvmfs/main.galaxyproject.org/deps/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/TruSeq3-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20
Using PrefixPair: ‘TACACTCTTTCCCTACACGACGCTCTTCCGATCT’ and ‘GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT’
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Exception in thread “main” java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at org.usadellab.trimmomatic.util.ConcatGZIPInputStream.read(ConcatGZIPInputStream.java:73)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:161)
at java.io.BufferedReader.readLine(BufferedReader.java:324)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:71)
at org.usadellab.trimmomatic.fastq.FastqParser.next(FastqParser.java:179)
at org.usadellab.trimmomatic.TrimmomaticPE.processSingleThreaded(TrimmomaticPE.java:63)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:311)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:539)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)


#2

Hi - The error might be a transient cluster issue or a problem with the fastq.gz input dataset.

  1. Have you tried at least one rerun to see if that resolves the problem?

  2. Are you certain that the problematic fastq.gz file was completely loaded? Please try reloading it as another test.

  3. If both fail, try uncompressing then recompressing the original file, then upload that to Galaxy and try Trimmomatic again.

Let’s start there and troubleshoot more if needed. Thanks!