Trimmomatic Failure

usegalaxy.org support
,
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)

1 Like
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!

1 Like
3

Hi,

I have samples run on 2 lanes which gave me two files each for forward and reverse. First, I concatenated forward files to one and reverse them into other. After this, I have run Fastqc for the quality which shows the format sanger/Illumina 1.9. Further, I wanted to run the Trimmomatic tool I got red error msg as below. I tried using trimmomatic tool using the files before concatenating and after. Both show the errors. please guide me.

Thank you

Vijay

Arguments:

  • -mx8G

  • -jar

  • /mnt/galaxy/tools/trimmomatic/0.32/pjbriggs/trimmomatic/f8a9a5eaca8a/trimmomatic-0.32.jar

  • PE

  • -threads

  • 4

  • -phred33

  • /mnt/galaxy/files/000/dataset_84.dat

  • /mnt/galaxy/files/000/dataset_83.dat

  • /mnt/galaxy/files/000/dat

4

Please, let’s keep everything in the same topic. Issues with Trimmomatic are very common in prior Q&A, so check that first, then follow-up in here if needed. "This is a new dataset and not all of its data are available yet" for 4 hours with trimmomatic